Star Fox (series)/WMG

Slippy is one of those frogs that can change gender a la Jurassic Park.
I can't remember where I read this, but it explains the Viewer Gender Confusion well enough, as well as the change in voice between 64 and Assault. Slippy would normally be male, but the single-gender environment triggered a gender change. After Krystal joined the team, it was no longer a single-gender environment and Slippy reverted to being male.
 * Hmm... unlikely, as his voice became male before Krystal joined (in Adventure).

Fox McCloud and Wolf O'Donnell are twin half-brothers from a failed menage a trois/date rape party.
They look too similar to be Identical Strangers, and their flying skill and choice in teammates seems to indicate some intimate connection to Fox's father, James. There's also the ambiguous reason for Wolf's hatred for Fox, which goes farther than It's Personal. As for the "twin half-brothers" part, it's possible (though highly unlikely) for one egg to be fertilized by two sperm from two different donors, which would account for the difference in species and coloring, while keeping the same exact look. Their difference in ages could be a case of one twin developing more slowly than the other, or an abortion gone wrong, or something.
 * Or they're fraternal twins who both take after their mother.
 * Or Wolf is James' younger brother (and Fox's uncle), which would explain the age difference and maybe even the rivalry with Fox (since James isn't around to pick on anymore).
 * Not possible, as Wolf is only a year older than Fox, making him the same age as Falco.
 * Or Wolf is James' illegitimate son and he resents Fox for having known their father.

Neither Wolf nor Leon are murderers and are actually loathe to hurt people, and thus their bounties are more for treason and other political war crimes.
Think about it: Leon constantly makes subtle threats to torture the Star Fox team if he captures them, yet his bounty is relatively low, not possible if he really was a bloodthirsty torturer. Also, Wolf specifically kicks Pigma out of the gang after Pigma's greed and unscrupulousness gets the better of him; only someone who distastes violence and cruelty would do that. Finally, after they get Panther on their team, we hardly hear of their freelance exploits, so they must not be that eager to flex their merc muscles again. Their vicious blood feud against Fox and Falco, respectively, might be the exception, but then again, those are almost assuredly personal matters.
 * Wolf's firing of Pigma may have had more to do with his greed getting in the way of his duty to the team. He seems like an efficient guy. (There might also have been a personality clash involved - Pigma doesn't look like he'd mesh well with the Affably Evil type.) Apart from that, while they may not be bloodthirsty psychopaths, there isn't much to suggest that any of team Star Wolf is actually opposed to hurting people, so long as there's a profit to be had.
 * It was stated in Star Fox Assault that Pigma was kicked out because of his overwhelming greed ind distrustful nature, so obviously there's something beyond merely his lust for money and about his actual motives that got the rest of the team on edge around him. There's also Leon's (unofficial?) comments during Super Smash Bros. Brawl, where he gushes over the beauties of a peaceful green planet being passed by, and how he'd love to settle down and have a family or whatnot. Then again, he did also state his desire for a The Masochism Tango-style relationship with Wolf, so maybe they're more tolerant of vicious bloodsports in the bed?
 * Or you know, Wolf is just an idiot and Leon is the actual smart one, and Leon knew about Pigma's motivations and convinced Wolf to get rid of him. After all, not every leader is able to see what's really going on.

Krystal and her people, or some other race similar to hers, used to live on Sauria (Dinosaur Planet) and died out/left it for some reason.
Think about it: Why else would there be magic gems and devices there that react to her staff? Why would Krystal have the power to ? How could any of the stone buildings and structures be built, if the planets' current inhabitants don't even have hands (like all the ladders, for instance)? Why the hell would the Warpstone even BE on Sauria? He can't warp dinosaurs, but he can warp Fox, which indicates that he was created by a race similar to foxes, but with magic powers -- Krystal's race. He even mentions that he was left alone for a thousand years -- probably because Krystal's people vanished that long ago, thus he had no-one to help.

The events of Star Fox Command were a hallucination created as a final ploy by the Aparoids to prevent their destruction by Fox and Star Wolf.
This explains the extreme and unexplained changes made to the continuity in-game: Bill's personality and voice, Kat's change in color, the inexplicable return of Star Wolf, Star Fox's breakup, Panther's sudden compulsion to refer to himself in the third person, etc. The hugely diverging storylines and endings give more credence to the fact that it's not real. The final nail in the coffin, though, is the developer's own hints that the next canonical game will take place in the middle of Command, essentially making half of the game's myriad storylines (and all of its endings) moot; this could possibly be used in the form of Fox and Star Wolf breaking out of their brainwashing and nuking the Aparoid Queen, as usual.
 * What I read is that the next game would make one of the endings canonical, though I also saw that it'd take place during Command. Of course, I read this over a year ago...
 * Also notable is the fact that Arwings can suddenly operate underwater with no loss in performance and the red dwarf becomes a volcanic planet for no adequately explained reason. Also notable is that the Starfox storyline is completely stupid and ridiculous for a game based on the shallow concept of blowing shit up.
 * Well, Command is pretty much accepted by many as non-existent, so as far as Assault goes, the story seems fine.

Wolf and Leon are gay sadomasochistic lovers.
No, seriously, it was confirmed in Super Smash Bros. Brawl. Apparently, Panther hasn't picked up on it, until then...
 * Heck, Wolf's outfit in Brawl is similar to a person who engages hot leather and BDSM.
 * This troper prefers to believe it's only a one-sided relationship. Leon is messed up by anyone's standards, but we have absolutely no idea if Wolf's reciprocated Leon's "affections".
 * This troper thinks it could be one-sided emotionally, but they're probably banging. Wolf strikes me as a gay adventurous Casanova (without the romantic layer Panther has).

Krystal is the remaining Cerinian from Cerinia's own Instrumentality.
Also, the entire Lylat system was seeded by EVA-01.

Fox was taking something illicit to calm his nerves for the final battle in SF 64, and SFSNES and SFSNES 2.
"Whoa, dude, I can totally see a monkey's head, and it has these giant hands with those gem things from Logan's Run. Look at how everything is moving in such a psychedelic way, man. And now the head is chewing my spaceship. Oh my god, dude, I'm totally freaking out. And holy crap, I can totally see my dead father." Anyone else notice that no one is around during these fights with Andross?
 * Ditto: The Awesome Black Hole -- depending on what happens after this level one of two things have occurred.
 * A: Fox was so under the influence whilst piloting an Arwing that he caused the whole team to get lost, when they find a way to get to Venom it's not the route they started out on. In one case, nearly overshooting their destination.
 * B: Fox was so under the influence whilst piloting an Arwing that he had a complete gap in memory between the checkpoint on the Astoroid Belt and entering Venom's Orbit.
 * Ditto: The Astoroid Belt (Hard), to the point where he has a 'white out' and comes to ! This doesn't explain why General Pepper can't contact the other Arwings unless...
 * The other wingmen were slaughtered, as the last thing you see the white out is overwhelming firepower from the enemy. An even more sinister turn of events would be that after the white out Fox killed his own wingmen.

Krystal's "tattoos" are not actually tattoos, but freeze brands.
Answering how a fur covered character can have tattoos, I present to you freeze brands. A type of branding that is supposed to be both more humane and less damaging than fire branding, freeze branding doesn't mark the skin, but it does hinder the skin's ability to grow fur or hair with any pigment. In other words, any new hair becomes white, just like Krystal's "tattoos."

A Timelord is involved somehow in Star Fox Adventures.
Mostly because I thought that Krozoa possession scene too similar to the snake in bed scene from "Doctor Who: the Movie" (Where a gray transparent slimy thing enters some American guy's body and makes his eyes turn funny colors); mostly because I want an alternate (Read: "less dumb") explanation for the plot instead of just "Magic".

Fox is descended from Batman
Just for the "Flying Fox" pun.

Lucy Hare has a daughter with Wolf O'Donnell
In one of the endings for Star Fox Command, Lucy Hare (Peppy Hare's daughter) has a daughter who ends up on the new Star Fox team founded by Fox's son Marcus. A picture of the team can be seen on Marcus' Arwingpedia page. Not only does Lucy's daughter have a familiar grey and white fur pattern, her eyes are the same color as Wolf's. Her aggressive stance also seems more like Wolf's than her mother's style.

The canon ending of Star FOX (SNES) lay
The reason that game does not marry up with the rest of the series -- which takes place in an alternate universe/reality. Fox, like his father before, got lost in an uncharted anomaly, never to be seen again. What makes this ending even more of a Downer Ending is that Fox doesn't see any of his wingmen after the incident and General Pepper is unable to contact any of the other Arwings, meaning As for the fate of Corneria, it's anyone's guess.
 * The implication more seems to be that the 'Andross' you face is a robot created by him (referred to as the "Core Brain"), and the real Andross is out there still... That said, Star FOX is a flight rail shooter - the story doesn't have to make complete sense! (Andross being a huge brain makes just about as much sense as him being a box inside a face made out of panels - my personal opinion is that these are both creations of Andross, at most remotely controlled by him.)

The James McCloud in F-Zero is a Legacy Character of the original James.
James' adventures took him far from his home galaxy, and along the way he met a young human who he became the mentor for, maybe like a second son. When the human heard of James's demise, he took the name and a similar name for his mercenary crew, and the outfit, out of admiration. Alternately, he's a Reincarnation. Or alternate universe counterpart. Or something.
 * Alternately, Andross didn't kill James, but instead made him human and sent him to Earth with a new ship. He started a family and modified his ship into a race craft. He races to provide for his family, and some day, Fox will discover the truth. Whether it drives him insane or does precisely nothing has yet to be discovered.

Sending Fox 'Out of this Dimension' in the original Star FOX (SNES) renders him completely insane.
Fox ends up in a strange cosmic anomaly where he is attacked by strange two dimensional creatures that ignore the normal laws of propulsion and physics. The distant alien planets and stars undulate wildly, barely comprehensible, and he is unable to get nearer to them no matter how far he flies. In the end, he fights a giant slot machine, and it is only when he scores a 'Jackpot', symbolizing his 'victory' over his own sanity, that the creatures cease to actively fight him. Simultaneously as the distant starry background solidifies to reveal smiling, peaceful faces across the planets, welcoming him, as only then does he truly 'understand'. There is no ending, though floating letters appear to taunt him with one, eternally reset both by the denizens of this universe or his own doomed attempts to right them. Fox is doomed to forever seek his end, unable to reach it as he flies through that warped dimension for eternity. Laughing...
 * Laughing...
 * Laughing...
 * ...and then crashes.

Star FOX and F-Zero take place in the same universe
Think about these two facts:
 * They share a technology known as the "G-Diffuser" system. In F-Zero, it's used to keep the race crafts off the ground (If only just); in Star Fox, it's used to keep flight craft aloft.
 * One character from each series is named "James McCloud". He suffers a Death by Origin Story in Star FOX, but he's still there in F-Zero. Maybe the two are related?
 * I'll give you one more -- the original F-Zero had race craft called the Golden Fox and the Blue Falcon. The Hero and The Lancer of the Star Fox Team are a golden fox and a blue falcon. Also, in one of the endings of Command, they outright join a racing league, called the G-Zero Grand Prix. Actually, this sounds less like they take place in the same universe and more like F-Zero takes place in the Lylat System in an Alternate Universe.

Andross may have thought that turning him into a full-fledged human would be A Fate Worse Than Death. Sending him off to Earth, an unfamiliar place, would have been the icing on the cake. James also had his memory erased, and he only remembers his name. The squadron "Galaxy Dog" was just a cover story, implanted in his mind just to give him a reason to own the ship he was given. However, knowledge of the G-Diffuser technology has awakened some old memories, and James is now thinking to what his life was in Lylat. He will eventually uncover the truth...

Star Fox and Star Wars have analogous characters
If it follows that Star Fox = Star Wolf then: and here's the big one
 * Fox = Luke Skywalker
 * Peppy = Obi Wan
 * Slippy = R2-D2
 * ROB 64 = C-3PO
 * Andross = The Emperor
 * Falco = Han ****ing Solo
 * Does this mean we're gonna see James McCloud return in armour and evil? (and to fit with the above, human?)
 * Given the WMGs of F-Zero, this could be entirely possible.

The boss of Sector X in 64 is a prototype of Andrew's Wannabe-Andross Mecha.
The prototype was abandoned in an early stage and was thus left unfinished. If you think about the shape of the robot, it's actually kinda believable.

Marcus McCloud is actually Wolf's son.
He seems to look more like Wolf than Fox. I'm guessing that Wolf raped Krystal at some point during her time with Star Wolf. Either Fox doesn't know, or he's just a nice enough guy that he helps raise Marcus as his own.
 * Why rape? Maybe Krystal was just really lonely and secretly wanted someone who was the next best thing to Fox.
 * Well, she sure didn't join Star Wolf because of Panther...
 * Yes she did! She did in the default ending of Command anyway, the one you have to get before you can choose your own path.(Maybe she'll aquire a bounty too and get shot down in a new game)

The Lylat System is in the same setting as F-Zero.
James being in F-Zero is simply because he faked his death at the hands of Andross to get a better shot at him. His son managed to do it instead, and he comes out of hiding to save him at the end of Star Fox 64. Seeing that he'd effectively passed the torch, he moved on to explore the galaxy.

As for why everyone in Star Fox is furry? Fox is mentally disturbed. Everyone is relatively humanoid, but we see the world through Fox's eyes, and he thinks everyone is an anthropomorphic animal. That's why he's a Fox named Fox, he's a human named Fox with delusions.

Albert Einstein didn't die.
Instead, he found a portal to another dimension where anthropomorphic animals ruled the universe. He was known there for inventing the Arwing, and Falco in particular was a fan of his.
 * Heck, maybe he got there using the Chronosphere

The Star Fox universe has its very own Einstein
The Lylat System has their version of an Einstein, someone with the same name who was really smart and invented important things (perhaps the G-diffuser system?). That's why Falco had such a reference point which would only otherwise exist in the real world.

James killed Wolf's father.
Wolf's father was the leader of a dangerous band of space pirates and James's team was hired to stop them. Wolf aligned with Andross afterwards to seek revenge on James and extended his hatred to Fox mostly by association.
 * Cycle of Revenge?
 * Perhaps the fact that Pigma, canonically the one who killed James McCloud, later joined Star Wolf isn't just coincidence? While Wolf would probably have preferred to kill James himself, he probably couldn't resist the idea of bribing one of James's own teammates to backstab him. It was only after he started hanging around with Pigma that Wolf started to hate him. Remember that the Worthy Opponent stuff is mostly from Assault onwards, too, so while Star Fox 64 Wolf may have tolerated Pigma, Assault Wolf probably couldn't stand him.

James is now an Energy Being or Reality Warper.
In the original Star FOX game, Pepper says that James flew into a Black Hole and was never seen again. But, in reality, James ascended after the Black Hole, he obtained new abilities, he rewrote Reality into Star Fox 64 in an attempt to raise the son he was never around, but he couldn't, so he faked his death at the hands of Andross, who tried to kill him to make sure that a Reality Warper didn't get in the way of his plot, but when Fox was in trouble, James, being his father, decided to try and help Fox in his darkest hour; afterwards, he disappeared again, trying not to make any other appearances until he's needed.
 * And in the meantime, kills time by racing F-Zero in human form?

Andross wasn't always a giant head.

 * Before his attack on Lylat, Andross was a neuroscientist who suffered brain damage through some sort of accident. During his career, he invented a serum that would cause the re-growth of brain cells in the hopes of curing his own brain damage by replacing his damaged cells with healthy ones without surgery. Recklessly, he gave the serum to himself. It worked; but his brain cells wouldn't stop growing, to the point where his brain would have burst out of his skull if not dealt with in time. He then had his brain removed and placed in a nutrient vat, where the isolation and artificial neuron growth made him go mad as his brain grew to massive proportions. Eventually, the serum wore off, and he had a giant robot head built to house his enormous brain, as well as a pair of hands.
 * Actually makes sense.

Krystal's back story is all in her head
Krystal just is a flaky, delusional, but otherwise normal attention whore. Her name isn't even Krystal - it's Norma Goldstein. Starting in her college days, Norma became enchanted by the supernatural. It was harmless, at first: she started wearing odd jewelry and gained an interest in the mystic practices of the obscure planet of Sauria. Then she claimed to have ESP, and legally changed her name to Krystal. Most of her old friends think the tipping point was when she permanently dyed herself blue and paraded around in a loincloth. Finally, after her obsessions and refusal to study got her kicked out of college, she declared that she was the last survivor of the mystics of Cerinia, rather than being the daughter of an office clerk in Corneria, and flew over to Sauria where coincidentally, Scales' coup was taking place.

When Krystal joined the Star Fox team, the other team members bought her story, mostly because Fox looked so hysterical when he was flustered. As time went on, however, her pretentiousness became too much to handle, but the team took it into stride anyway. Sometime after Assault, however, the truth was revealed when Krystal's old landlord saw her a news report on the Star Fox team, and demanded that Norma Goldstein pay her long-overdue rent and reparations for her apartment. Only Fox believed her story after that. This is why Krystal left the Star Fox team before Command, and why her parents are never mentioned again.
 * So how did she know what was happening on Sauria during the Aparoid War?
 * One possibility was that she actually gained powers during this time - kind of like what happened to Oda Mae from Ghost, where she was faking it at first, only to gain it for real later on.
 * Wait, something has to explain the magic but possibly high-tech staff she was carrying around at the begining of the game. Where did she find it? Could it be a Krazoa artifact? If she didnt find it in Sauria, does that mean that the Krazoa were the previous inhabitants of Lylat?

The Star Fox team in 64 aren't actually in their Arwings.
Other than during the Blue Marine mission, they're actually all crammed inside the Great Fox, remotely controlling the ships from a safe distance, handily explaining why they never seem to die. They only had one Blue Marine, and since the water is so dark, they just sent Fox and Falco in.
 * Actually, if Fox is shot down when no teammates are around, he screams before his Arwing explodes.

Star Wolf presumably isn't doing the same, what with them requiring patching up on Venom II.
 * That, and the fact the mechanical stuff also serves as dampeners so they could handle their new ships pretty much confirms they weren't.

James isn't dead
In the original Star FOX, there was a bonus level called 'The Black Hole', where James appeared to died, but after the level, you get teleported to Venom. I personally think it was a WOR Mhole, not a Black Hole. BLAC Kholes are space vacuums, and WOR Mholes are like intergalactic highways. So essentially,

Fox and Fara are half-siblings.
And this is why Fara is a dead ringer for Fox's mother Vixy. Fara may also be at least a year older than Fox. See, maybe Vixy became pregnant shortly after (or maybe even before) James and Vixy were married. But some time before, Vixy may have been pregnant with Fara (probably by an old boyfriend), and gave the child up for adoption to Fara's father the shipping magnate. Vixy later met and married James, and Vixy left the incident in the past. Of course, this is also only Brother-Sister Incest if you actually think Fox and Fara started dating, which this troper is skeptical of.

Fox is pansexual and polyamorous.
But not for Anything That Moves. He actually has a fairly passionate heart and can fall in love rather easily if the chemistry is right. He probably has a separate semi-casual non-exclusive relationship each with Falco and Wolf, but probably truly loves them too. There are variations of this theory with my friends -- some say just with Falco, some say just with Wolf, or some say Fox really does nail Anything That Moves.

Falco is Invisible to Gaydar.
I mean, there are certainly many canonical details that suggest its plausibility, but my theory solidifies it, so this has relatively more confidence than ordinary WMG. You see, he and Katt are more Like Brother and Sister, and they care about each other and love each other in that capacity -- this is Played Straight. Falco is Katt's Gay Best Friend, but for a long time Katt was strongly in love with Falco, which he could never requite. Falco for his part just wants her to grow up and move on as a strong independent woman, and it appears she eventually does (and also begins to fall in love with Cool instead). Falco is not interested in girls, nor is he interested in relationships in general. Now getting increasingly less canonical and more fanonical. Though he's not into relationships, Falco still forms them, but may downplay their significance. (What makes this different from Katt? Falco has no Unresolved Sexual Tension with Katt, but Fox and Falco appear at times to have Belligerent Sexual Tension, probably with plenty of Slap Slap Kiss.) Since Fox and Falco are the Fan-Preferred Couple in Japan, I'm going to say that they actually are a couple -- not formally committed, and not merely Friends with Benefits, but more like Best Friends With Best Benefits, Like an Old Married Couple. Falco refuses to quantify these things, and Fox doesn't even try to make him (he probably isn't one to talk), but their relationship simply takes the paths it takes. Falco could be there all the time, or away for a long time (even years, such as after Farewell), and it's not like this upsets Fox's life too much. The love may be epic, but the romance is not.
 * This should so be said in the games somewhere. I'm glad I'm not the only one who thinks this.
 * Really? On some forums I've been to, the notion that any of the characters could be gay is immediate Flame Bait. Even Wolf and Leon, even when you show them proof. Strangely, there is little Flame Bait when someone suggests that Slippy is either gay or a woman or both, when Slippy is the one character furthest away from tripping my Gaydar. Or Andrew. Basically, any character they don't like. Makes me wanna bang my head against a wall repeatedly. It appears the Japanese and American fandoms have very, very little in common culturally.

James and Peppy were lovers.
As both widowers and single dads who lost their wives at young ages, it is not completely inconceivable that the two fell in love. It is even possible that they moved in together, and helped raise each other's kids. This makes Fox and Lucy more like step-siblings, and Peppy more like Fox's other dad. The moving-in part wouldn't have happened completely until later, because though Fox's mom Vixy died when he was a baby, Lucy's mom Vivian died when she was an adolescent.

Wolf was once part of Star Fox with James, Peppy, and Pigma, and James scarred Wolf's eye.
But if Wolf was part of Star Fox, he would have been just barely an adult, and he would have been the first member to leave. Wolf's leaving occurred during a spectacularly low point with the team, and James scarred Wolf's eye. From then on, they were enemies. Variations of this theory differ as to whether James and Wolf were also sleeping together.

There is nothing particularly unusual about Slippy.
Really. He's not a woman. He doesn't even have a high voice. And he's straight. He could even possibly be the only male member of Star Fox who is straight. And he's actually fun to be around, but his portrayals have usually been very unflattering. And he still wears that bead Utility Necklace, but artists have simply chosen not to draw it.

Venom is a decaying terraformation.
Venom was Terraformed in the distant past. But terraformations can be unstable, and a planet's chemistry and climate can gradually slide back to its unterraformed state if there is no maintenance. (This is considered realistic for Mars -- even if it is terraformed, it will revert after some millions of years.) Specifically, Venom was given an atmosphere and oceans, and they were once stable. But the planet's technological infrastructure was abandoned and the terraformation was left derelict. Gradually, the chemistry absorbed natural minerals from the bedrock, turning the air and oceans into a noxious green poison. An alternate theory using the SNES continuity, is that Venom's toxicity is a much more recent occurrence under Andross's rule, and that the Lizard Folk used as Andross's Redshirt Army were the indigenous inhabitants of a once-clean Venom.

The LylatSystem has planets originally from other star systems.
An ancient civilization (probably the same that throve three million years prior on Titania and Aquas) not only Terraformed some planets, but hauled in more planets from other star systems, probably using jumpgates of a scale immensely larger than Beltino Orbital Gate. Otherwise, doesn't it look like the Lylat System has a very unrealistically high number of habitable earth-like planets?

The Cornerians were originally humans from Earth.
Maybe they are actually originally Petting Zoo Humans from Earth, and did not evolve on Corneria or anywhere else in the Lylat System. They either found their way there, or were brought there by others. Though they more resemble Funny Animals, they are actually human, and can procreate with other "species" within the same Amazing Technicolor Population. Andross's Lizard Folk (who are not from Corneria) are also human.
 * They were brought there by a Goa'uld who wanted to create a variety of colorful hosts for himself, and thus genetically modified a number of humans to superficially resemble other species from earth. The hypergate is similar to the Ori supergate, but has an extremely limited range due to lack of available power.

The events of Adventures, Assault, and Command were really Wolf's nightmare, and never really happened.
Neither the Anglars, the Aparoids, Cerinia, Krystal, Sauria, nor Tricky exist. The events of Adventures, Assault and Command never happened. Farewell, Beloved Falco actually did happen, but Wolf was not there and it did not factor into his dreams. Amanda, Dash, Lucy, and Panther also actually exist, as Wolf knew about them. Since the Lylat War, the Star Fox and Star Wolf teams had had occasional peaceful interaction -- Fox and Wolf were still rivals, but they came to respect each other in peace time. Andrew and Pigma had left Star Wolf, and Panther had joined (though Panther had not yet met the Star Fox team at the time). The night of the nightmare was a very slow night when Wolf, Leon and Panther had nothing better to do than play a Zelda game all evening. That night, Wolf dreamt a long and detailed dream -- it might not have been a nightmare, except there was always this incessantly irritating blue vixen who wouldn't shut up and wouldn't go away.

Star Fox 64 3DS is the beginning of a series reboot.
They saw the complaints about Adventures and Assault, and that most of the fanbase hates Krystal. As such, they decided to retcon Krystal and the games she was in out of existence. The series is starting over.
 * Agreed, Krystal is very divisive, and pretty unpopular at least in Japan. But she remains wildly popular in the West, with most anti-Krystal fans being pre-Adventures fans, female fans and the powerful gay fandom. The topic of Krystal is a Holy War, where her Fandom and Hatedom cannot compromise and cannot coexist peacefully. So it seems likely that no matter what the creators decide to do, someone will be very unhappy with it.
 * It doesn't help that Nintendo has absolutely no idea how to mold her character. Your average ten percenter has a better chance of giving Krystal a good backstory and/or personality.
 * I'd have to completely agree, seeing as they completely pretty much screwed over all characters in Command.

Lylat is NOT a binary or triad star system...
...it's actually a group of systems under the control of an organization that has titled the area Lylat: Corneria is the capital of the Lylat territory, and Venom is a backwater toxic world on the outskirts. Because there's no way to figure out how to fit all those planets in the same system (with that itty-bitty red dwarf for a sun, no less!) otherwise.

James McCloud has robotic eyes
He lost them in a tragic accident/flying mishap years ago, back when Fox was little. And because the glowing false eyes scared little Fox, James started wearing his Cool Shades all the time.

James is an Immortal
ala Highlander. Andross killed him after he helped Peppy escape, but didn't cut his head off, so James was able to escape when no one thought to keep an eye on his body. James just lurks around Venom in his Arwing because he knows he has no way to explain why he's still alive. James uses his ''sword? what sword?'' powers (from the series if not the movie) to hide his Arwing, which is why no one can see him. And the reason Fox can sometimes see James when no one else can...well, he's an Immortal too. But he doesn't know it/hasn't died yet, so he doesn't understand why he keeps 'hallucinating' that his dad has been helping him all those times.

Fox is descended from a Cerinian
Several thousand years before the events of the first game, a Cerinian ended up in the Lylat system and had children with one of the people there. Over time, the Cerinian traits would slowly disappear, but would still remain dormant in the ones who had it. This is how Fox is able to use Krystal's staff and be able to pass the tests of the Krazoa. It also explain how he can see James while the others can't.

Star Fox 64 3DS is not just a remake of 64
But will include a remake of 2.
 * Not likely, but still. I like this one.

The shopkeeper will be the new primary antagonist of the series.
She was secretly planning on warping herself into an Eldritch Abomination, the likes of which only seen by Pathways into Darkness. She only was staying in that store to collect scarabs. She had no intention of helping Fox out at all, she only wanted him to give her scarabs. Scarabs with which to further her perverse plan. This plan will involve taking innocent people from the Lylat system and then separating their bodies, mind, and soul from each other, twisting them into an Eldritch Abomination. Their bodies will be twisted into mechanical constructs that would be worthy of an H.R. Giger or Darkseed style mindscrew. (Albeit with less phallic emphasis). Some people will have parts removed from their bodies, and she is not one to waste them. She will graft them onto the next Eldritch Abomination she creates. The minds of her victims are twisted with the pain of being separated from the soul, and are sewn into other abominations of her creation... the very scarabs that Fox was giving to her in exchange for the items she had. It is a fate worse than death, as these scarabs will have their will removed, only being able to think about how much they must pay her. The soul, however, from the pain inflicted on it by being separated from the mind and body, are used as the building blocks of her own dimension, an Eldritch Location. From there, the evil witch plots her next move...knowing fully well that she cannot be traced into this dimension at all, and if anyone dares follow her, they will be forced to withstand the most brutal deconstruction of the Nostalgia Filter of all time. Not only will you be forced to see your own childhood, but every trauma will be replayed to you, and any joy you had when you were a child will be twisted, perverted, and demented into a tempest of incredible horror. Even when Fox enters, he will relive everything, from the fight against Andrew to Pigma twisted into a giant monster by the Aparoids. The people who are trapped in this dimension eventually lose all semblence of humanity or anthro-nity, and their sanity, too. They are reduced to a shell of their former self, almost reduced into toys or other such stuff. Fox will encounter other expeditions sent into this dimension, with only stuff like a plush toy moaning to themselves, a deflated pool toy that was once somebody else, an expedition leader turned into an Unobtanium statue out of fear, insane people who have merely frozen in place, twisted clockwork people, people who have, out of fear, been reanimated into zombies after taking their own lives, or risking a pain worse than death, forced into a quantum immortality even as their physical form is warped into that of a demented toy or worse. The evil shopkeeper by this point had merged with this dimension, becoming something that would be most comparable to Giygas or Cthulhu. She tugs at his own sanity, as well as the sanity of everyone else, as they are forced to stand up to her, separated from their friends and comrades and forced to fight the evil demented goddess of this hellish dimension all by themselves. In their mind? Fox, Krystal, Falco, Slippy and the others? They're dead. Deader Than Dead. But they do not know where they truly are... And yet Fox will be bothered because, after all, he could have prevented this, if only he had just taken out that staff and killed that witch back on Dinosaur Planet. But on the plus side, Prince Tricky will have been twisted into a deliberately annoying abomination and will be a mid-game boss, so I guess that balances all of the horror out.
 * You seem to have thought about this for some time.... Actually, when you think of it, Star Fox Command may be part of her sick-mind games that she inflicts on Fox. Also it could also be that the Krazoa Spirits were collaborating with the shopkeeper from the start, along with General Scales, to deliberately set Fox onward on his quest on Dinosaur Planet. General Scales, as the shopkeeper's right-hand man, threatened Dinosaur Planet in order to lure the Star Fox team to Dinosaur Planet; while the Krazoa Spirits set Fox upon a complex quest to gather scarabs for there master, disguised as a quest to save Krystal and bring Dinosaur Planet back together. In the end, the shopkeeper used some of the newly amassed scarabs to draw up enough power to create a decoy enemy to avert any suspession from herself, and crafted this decoy enemy in the shape of Andross from Fox's memories. In this way, General Scales could fake his death and return back to his master alive; and later to further make sure that she would not be opposed, she created the Aparoids to weaken the Lylat system's military forces. It is still up in the air if there is any hope of stopping her now at her full power though...
 * Actually I kinda just improvised that all as I went along - but your theory makes just as much sense there, heehee.

Falco hatched from a mutated egg from the depths of the Zoness ocean.

 * It pretty much explains why he has such a fetish for flying, is kind of a prick, and is the only member of Fox's team without ANY mention of a family...
 * And why Katt wants him.
 * Probably not a mutated egg, since Zoness' pollution was explicitly caused by Andross, and Falco was born long before that. Maybe Zoness has (had?) a sentient bird species that Falco is a member of. That said, Falco being a Zoness native does put his "This is horrible..." line in a new light: he knew what the planet was like before it was ruined.

Wolf is an albino who dyes his fur.

 * He has Purple Eyes, but a lot of Fan Art (and Star Fox 2 portrait) shows him with Red Eyes, Take Warning. He doesn't want to look colorless, so he regularly dyes his fur a purplish hue of grey. ...yeah, even I don't believe this one, Wild Mass Guessing is just fun to do.

Star Fox SNES and Star Fox 64 are parallel universes.
This might explain how the characters have different ages. Assault may be yet a third parallel universe, where Wolf is six years older than he should be. Or maybe Star Fox is just competing with Star Trek in sheer number of Retcons. There's so much canonical flipflopping you'd think it was a pancake house.

Command is actually in the same canon as the first two Star Fox games (Star Fox and the unreleased Star Fox 2)
This explains why the characters differ a bit in personality and other traits such as accents. Panther being a rather good example of this. Also, they used the art work from the original Star Fox for the team members at the beginning of Command, which could be a hit toward the place of the game in canon.

The Gola from Titania is part of a species similar to the Aparoids.
I mean, think about it. It's a giant insect, it uses lasers to attack (the Aparoids are technologically advanced), and its chest looks a little like an Aparoid Core Memory. Also, its scream is very close to that of the Aparoid boss from Katina.
 * If you're confused about how Aparoids may have ended up on Titania, here's what I think. Originally, Titania wasn't a desert world. That much is canon. So, when the Aparoids got there, they assimilated the beings there. However, without living things that cared to maintain it, the plant life died out. The result was a desert, and combined with the wind and its proximity to Solar, it became inhospitable. So, the Aparoids had to evolve, over time becoming less and less flight-based and more ground-based. This also seperated them from the Hive Mind, since their molecular structure lost the self-destruction cells that also linked them, thus sparing them when the Queen was killed. Eventually, they became large beasts that were almost completely different from the Aparoids.

James McCloud survived his trip into the black hole and actually experienced time dilation instead
James after seeing Peppy Hare was safely away and realizing he was dead either way decided to take out as many of Andross's ships as possible and tricked them into flying into the black hole by flying close enough to the gravitational field to pull in the bigger ships chasing him. It was mostly though sheer luck he survived. After the time dilation wore off he found himself in the middle of the battle over Venom and after seeing what he assumed to be a military force sent to stop Andross's planned invasion engaging Venom's forces. He then used the confusion to enter the path to Venom's core where he arrived in time to see his son destroy Andross and then lead him out of the core. Then deciding that his son was his own man now and didn't need his father anymore, he maneuvered his Arwing into Fox's blind spot and then made a run across the surface of Venom until he was out of range. James decided to roam the galaxy as a gun for hire, eventually becoming a race car driver on a distant planet. Slight variation of the a theory above in which it was a wormhole instead of a black hole.

Wolf holds a grudge against Star Fox because he wanted to fly with James McCloud, but was turned down because he was too young.
Wolf grew up on the streets in a similar fashion to Falco and met James McCloud (or maybe heard of him depending on how legendary James's reputation was at the time) and decided he wanted to fly with him. James turned him down for any number of reasons, ranging from Wolf being to young to James's disliking his methods. Wolf became bitter about being turned down and when he learned of James's death Wolf kept his grudge against team Star Fox as a whole. Which is why he has a rivalry with Fox.

Star Fox is a cartoon adaptation of the real Star Fox team
The "real" Star Fox team are humans, as is the rest of the intelligent population of the Lylat System (save Sauria). However, when the team allowed their likenesses to be used in a Saturday Morning Cartoon, the producers decided to make everybody animals, since kids would probably find them more interesting that way.

Also, to make the team seem less morally ambiguous, a plot point was added where Andross killed Fox's father James, so that Fox would have a personal (rather than monetary) reason to defeat him. Of course, this doesn't end up making much sense to the viewers of the show, since everyone knows that the real James is not only still alive, but became a well-known F-Zero pilot after retiring from mercenary work.
 * Holy shit.

Treasure will tackle the next Starfox game on the Wii U.

 * You know the guys who made: Gunstar Heroes, Ikaruga, Sin&Punishment? They have the skills to actually make a good Starfox! Also, I would to see some a lot Shout-Out, like they always do.

James McCloud is blind.
Sunglasses are normal for a blind person to wear. He can still fly because he has a Disability Superpower. His quotes from Command suggest this.

How Bomb Spore Plants grow.
Okay, I'm no plant biologist, and would never claim to be, but I think these plants have a couple of interesting properties.
 * 1) "Fully-grown" specimens have grass growing right up to the base. The planting patches for the spores, by contrast, are pretty barren.
 * 2) Fully-grown plants throw out spores when detonated. Young ones do not.
 * 3) Fully-grown plants grow back immediately after being detonated. Young ones do not.
 * What this suggests to me is that Bomb Spore Plants, when young, require a very specific mixture of soil that other plants can't grow in. Then, as they mature, they change the soil mixture into that which things like grass can grow in. If we were to leave them alone for long enough, they, too, would develop spores, and well as grow roots that allow them to recover quickly from being detonated and allow them to thrive in the changed soil. Of course, the game wouldn't model this, as you're intended to detonate them shortly after planting them. Now, if only I could figure out why ideal planting patches tend to be found beside things that Bomb Spore Plants can destroy...

Corneria has little to no standing army
Hence why and a few other things. Bill and generic "Dog Solder" are in-fact militia (hence why they are so utterly inept). This explains how the capital is so easily attacked regularly as well. The only problem I see with this is the "we'd be honored to have you as part of..." at the end of 64, which can be explained as only officers having an actual state military career, while giving Fox an invitation to join.
 * Mercs make up the main offensive forces of any military action.
 * A prominent merc can simply become a general in a few years.

ROB and Great Fox are permanently linked, and Fox chose to free them after the Star Fox team broke up
While he is permitted to leave at any time, ROB chose to stay at Fox's side in lieu of anything else to do with the vessel. However, in the event that he finds something else worth his attention, it is accepted that he may head off to investigate... and take the Great Fox with him.

In fact, he's the main playable character in Star Fox Command, and when you have split path options like "I wonder what Falco's up to", ROB is actually flying the Great Fox to his position.

Krystal will become a permanent member of Star Wolf.
It is what she does in the default ending of Star Fox Command, to be with her beloved Panther. If Star Fox does not become a power trio she'll probably be replaced by Amanda or Kat. New characters are a possibility too.