Treasure Planet/WMG

Titan AE and Treasure Planet take place in the same universe.
Disregarding how eerily similar the characters, settings and plots are, Earth having been destroyed and humans being scattered across the galaxy would totally explain why Jim and his mom are the only humans we see in Treasure Planet at all. And not on Earth.

Related to the above WMG, Mass Effect and Treasure Planet take place in the same universe.
How the ships get across the galaxy so fast is because they use off-screen Mass Relays to get around. And doesn't Captain Flint look like a cross between a turian and a yahg? Also, several other aliens in Treasure planet look like strange salarians and hanar, so it could happen thousands of years after Mass Effect 3.

Joseph Korso is Jim's estranged biological father.
Consider the above... and think about it. It just fits too well.

Jim's mom was a street rat.
She's very focused on keeping what she has, and making sure Jim has a future. In addition, she delivers a Full Name Ultimatum to Jim for bringing someone random in, but goes over to help immediately when he says, "Mom, he's hurt." She was The Heart of her Ragtag Bunch of Misfits, and slowly evolved into a Team Mom, meaning that her reflex is still to help people--because you don't leave anyone behind. She and Jim's dad met because he helped them out, and the house was his. When his parents disowned him for marrying below his station, that was all they got to keep, and they fixed it up into an inn together. That's the real reason Dr. Doppler is apologizing to her about the inn--not only is it important in that it's her livelihood, she built it with her own two hands when she and her husband were still together. This made the fire a Trigger both because she was completely losing the last of him, and a childhood trauma with fire, hece why she acts more out-of-control in that scene than any other. Jim's suggestion of rebuilding the Benbow Inn with the money he could make is met with a sigh because she's trying to figure out whether she should explain why it was important to her.

...Hm. I've just written a messy outline for a fanfic, haven't I?
 * Oh hell yes. Permission to use, given time to finish what I've got?

Jim's father left because he got bored.
Same troper who wrote above, and if the theoretical fanfic gets written this would be included. He was interested in leaving home because he felt stifled, but found it wasn't as adventurous as he thought. The boat was either taking him on his next adventure, or back to his wealthy parents, who would un-disown him if he divorced his wife and left his son.

Jim's mom just wants to make sure he doesn't Turn Out Like His Father.
Jim's dad left on that boat, so she associated leaving like that with leaving in finality. She's worried he'll end up going on one adventure after another and--depending on what you think his father was doing--ending up getting rich and leaving her alone, or getting a taste for adventure and leaving her alone.

Scroop isn't as bad of a guy as we are lead to believe.
In the all of 8 minutes of screen time he has, he does NOTHING that any of the rest of crew (Save for the protagonists) didn't already do/wouldn't have done (IE threaten Jim, question silver's leadership, Lie). His big Moral Event Horizon moment was killing a pompus, brown nosing dick, and have it blamed on Jim (Because structural failure of ropes apparently doesn't happen in this universe), while bad, Silver and the others burned down the Inn, that they KNEW had people in it. Far worse.
 * Except the other half of the rope was actually missing, so it didn't look like it broke, it came undone.

Delbert and Amelia are the same species.
If they belong to a species with doglike males and catlike females, it would explain how they are able to have children and why their daughters resemble Amelia while their son resembles Delbert.
 * Dogs and cats? Living TOGETHER?! Mass hysteria...

Not only are Delbert and Amelia the same species, but Silver as well.
Aside from all being more or less similar in skin tone and all sharing the same amount of arms, heads, eyes, mouths, etc,(which is saying a lot given the diversity of species in this movie), Silver also seems to be somewhat canine, like Doppler. Silver probably looked more like Delbert in his youth, but he's really let himself go over the years.

In this universe Space Air exists.
There is air in space but without gravity, artificial or otherwise, it's at too low a pressure to breathe. Spacesuits like Delbert's exist for people working in conditions without artificial gravity to compress the air. When artificial gravity is turned off, people rise because the compressed air around the ship is trying to escape and is carrying them with it.
 * Unfortunately, the air would depressurize in milliseconds in that circumstance, so it doesn't work unless you postulate that the air moves much more sluggishly than it does on Earth, in which case you have to wonder how people are able to breathe....
 * maybe there is just a MASSIVE amount of air?

The Forerunners from Halo made treasure planet.
Because why not?
 * Because it is just too awesome for one story to handle.
 * Considering what is known of the Forerunners in the Halo universe, its entirely possible. After all, artificial planets and massive cross-space portals are both mentioned and actually seen in both the Halo books and the games. As well as the known fact that the Forerunners explored other universes besides their own. Not to mention Jim, a human, is the only one who seems to be able to operate the map. Just like.

Morph is an Alternate Universe counterpart to Envy
It makes sense: Envy could be Morph's Evil Twin in a different world. Both are Shape Shifters and both have at least worked for the bad guy (in Morph's case, it was Silver). Then there's

Jim's father would have returned.
If he hadn't met with an unfortunate end while off on a grand adventure. Considering Jim's mother's reaction when he left (sitting at the table crying), it was likely something with a very high risk to it, and a high chance of him not coming back - much like Jim going off to chase down Treasure Planet. Young Jim, not quite understanding the full extent of things right then, just knew that his father was leaving to do something extremely dangerous. He chased after him that morning to try and get him to stay. Either that, or, with all the exciting stories his father brought home with him, wanted to have an adventure of his own.
 * Reading that, I was suddenly reminded of Kamina. *Head Asplodes from the Awesome* (Heh. Jim's dad really got around didn't he?)