Mega Man ZX/WMG

Zero didn't die at the end of Zero 4, but YOU Killed Zero in ZX.
Zero survived the end of Mega Man Zero 4, and "Omega" is the remains of him. Zero was heavily injured at the end, and lost his helmet. He eventually came across a wandering Omega and destroyed him, and took his armor. Thus, YOU KILLED ZERO.
 * Then why did he yell the messiah line?
 * Not only that, but why would Zero try to kill you? How would he go about merging with Omega? Where was he all this time? Gonna use that "I hid myself so I could repair myself" excuse from X6, again?

The Sage Trinity are the doctors from the Classic series.
Their Disk data says they were Human, taking on bionic bodies to let them live for centuries. Note the plural; ZX takes place 100 years after Zero, which takes place 100 years after X, which takes place 100 years after Classic.
 * By that token, Master  went insane with grief after living so long and seeing   and decided there was no better option than to start over by resetting the world.
 * This...this makes so much sense, and would tie up a lot of loose ends.

Megaman ZX 3...
...will be made and star Neige's daughter, who will Megamerge with Model C(raft). Just because it would be so cool.
 * Wouldn't she need to be immortal to pull that off? I mean, the ZX series takes place about a thousand years (Or was it a few hundred? I forget.) after the Zero series and Reploids have human-like mortality now and humans only got robotic bodies. In fact, if I'm not mistaken, the only beings that were immortal were Prairie (for some reason), the Sage Trinity, and possibly Grey (since he was created by Albert).
 * I believe it's around 200 years. Given that humans were given cybernetic enhancements, I wouldn't be surprised if Ciel exists out there.

Guesses for future ZX installments, mainly the final one
Character wise...
 * At least one new character will use a Model B, but if they are a Final Boss/ Disc One Final Boss then they will stay hidden until their battle and reveal that Model B is Model Bass. Bonus points if a Treble Support System is used.
 * For at least part of the plot, you will play as either the Model X user or the Model A user of your gender choice.
 * If you continue using Grey/Ashe, one of them will find a romantic interest in one of the other Mega Men (Atlas or Aile for Grey, Any of the others for Ashe).
 * You will be forced to fight Model Z or alternatively, Zero with a new body, at some point... unless he ends up being the star of the next game.
 * Model X and Model A will start thinking about who Model A's based off, as Model X is reminded of Axl
 * Girouette will get rebuilt and come back just like Zero did all those times (basing this off of nothing expect for the fact that it would be another way to compare the two).
 * You play as two previously-unknown characters who are revealed to be the memory-wiped Prometheus and Pandora, who eventually regain their powers.

Plot wise...
 * Thomas will continue the Games of Destiny, but as a distraction from his main plan. This will be screwed up in one way or another.
 * Model A will have an identity crisis at some point.
 * The creation of the Carbons will either be involved or hinted at.

Boss wise...
 * If they don't return as good guys, Pandora and Prometheus will come back either Brainwashed and Crazy or in a damaged/falling apart form, possibly combined.
 * Omega will make a reappearance, though he may or may not be an Anticlimax Boss
 * The other four model users will be upgraded, but at the same time, due to their own Models fighting back, having second thoughts about the whole thing.
 * The Model W pieces will be used by Thomas, but instead of the form's Albert took initially Thomas's will be reminiscent of Weil.
 * Eventually, somehow, Wily will manage to construct himself a new body out of the Model W parts, becoming the series TRUE final boss and the mastermind behind pretty much everything. Bonus points if it ends up Mikhail was Willy all along and had manipulated both Albert and Thomas all along, perhaps even remarking to Thomas "Just like old times eh Light?" If Thomas does end up being Dr. Light.
 * Also, Wily will fight using a Model W form that resembles a Wily Capsule, then in hand-to-hand combat. As he bows his head and begs for mercy, you kill him execution style.

More guesses about the next ZX game/s (should they ever come out)

 * Ciel is still alive: Vent's storyline reveals a possiblity that she managed to escape Serpent's attack, and while Aile's storyline is usually considered more canonical, I think it's pretty safe to assume that the different details revealed about the past are supposed to complement each other. And it was already established that humans can possibly live for hundreds of years via mechanical implants.
 * Prometheus and Pandora will return, even if they were intended to die in ZXA, they will be Saved by the Fans.
 * There will be a new Model Z biomatch, and you will be able to choose between playing as Vent/Aile(with model X, gaining powerups by reclaiming the Biometals and/or unlocking Model X's Mega Manning power), Grey/Ashe(with Model A, gaining powerups via A-Trans like in ZXA) and the new Model Z user/s(who will learn new moves by beating bosses, like Zero).
 * Weil will hijack the plot: Because that's a series tradition, and given the backstory, it will probably happen at some point.

Siarnaq's goal on the Game Of Destiny
Judging from his info from the Datadisk, he was backstabbed and Left for Dead in the past, and he becomes cold and impassive. With that, maybe he thinks that Humans Are the Real Monsters and then he tried to wipe out humanity?

Alternatively, when we lose to him in his boss battle, he said that he's proceeding to take over the Legion. What will he do with that?
 * Perhaps he removed his personality because he was sick of feeling the effects of betrayal and pain.

Master Albert is Doctor Wily
Albert? Wily? Come on, it can't be a coincidence! At some point, Wily became an Omnicidal Maniac who is using the biometals(even Model W) to "reset the world", because he hates the fact Dr Light's legacy has managed to integrate with even human bodies, and that no-one remembers him. He's taken a step in Magnificent Bastard.
 * Model Z could also integrate with human bodies.
 * The problem with Master Albert being Doctor Wily himself is the same as the problem with Dr. Weil being Dr. Wily. How did Wily manage to live throughout the entire Mega Man X series, up until the Zero series (and in this case, beyond that) on his own? If he was Weil he had to survive until he was given the cyborg body by Neo Arcadia, in the which case their punishment- a body that refused to let him die- would be lessened. If he's Master Albert, how did Wily live roughly half a millennium without being discovered on a planet that's had at least one colony dropped on it?
 * Time machine. Wily's had access to one before. Now why he chose to stay in the future, THAT'S another question.

Master Mikhael is evil
The other two are. If we wasn't evil to begin with he'll probably become an evil mastermind out of sheer peer pressure.

Mega Man ZX 3 will star a new Mega Man...
...who will Megamerge will Model V(ile). Who will have his/her own Ride Armor. You know you want this to happen.

More unhinged predictions for the third game, Proto version
At one point during the gme, perhaps at the end of the final boss fight, the player will be helpless, perhaps due to Model W energy, perhaps due to any number of things. then, just as it looks like they're going to be finished off, a familiar, but slightly distorted sounding whistle sounds off as Protoman, damage and looking a bit mix and match in regards to parts, pulls off a Big Damn Heroes. Double points if all he did was expose himself to the boss and the Main Character finishes things off ala MMZ 3.

Alternatively, Protoman is behind everything.

One big Sage Trinity theory.
Alright, we've already explored the idea of the Sage Trinity being the original doctors. Now, let's go a little further. To do so, I will be in character.
 * Master Albert: Mwhahahahaha! I am the great Mad Scientist, Dr Albert Wily! Now, you're probably wondering what the hell happened to me. After they designed the Mother Elf, I came to the conclusion that it could make me Deader Than Dead. I wasn't going to take it, so I became programming. And now I'm back, ready to Take Over the World via Model W. "Model W/Dr Weil was manipulating me?", you say? FOOLS! HE IS NOTHING COMPARED TO ME! I manipulated that retched excuse for a human being and he doesn't even know it. Yes, I called him retched. I may be power-hungry and prideful, but I ain't a sadistic ego-maniac! Oh, and tell Model Z I said hi.
 * Master Thomas: Everlasting peace. Yes, I once believed that. Oh, I believed that. But then came the Elf Wars. Then came the pain and horror and blood and suffering. The world turned into Hell. Being a Literal Pacifist can no longer work. I needed to desperately heal the world. I needed save the world. The only way this can work is if the planet is reset. To be back to what the world was like before Wily and I went at it.
 * Master Mikhail: Bah! I've been completely forgetten. But it doesn't matter. I can save the world.
 * Alternately: Light can't do what he needs to do all alone. He needs help. He needs me.

Thetis is not evil
He was, at worst, a well intentioned extremist after he joined the game of destiny. Keep in mind that he would have been directly recruited, then, by the man running the whole game, prometheus, or pandora. My theory is he only started trying to wipe out humans after he came into contact with someone who had a powerful connection to Model w. Unfortunately for poor Thetis, this implies some things were done to him to make him more acepting of the implications of the game of destiny.