So Tony is going to be his counterpart from comics-verse
Earth-3490. Which means he's going to be Natasha Stark-Rogers, aka Iron Woman, and married to Captain America, averting the Civil War in the process. :D I am still sorting out exactly what the timeline here is going to be, but I'll add it to this post when I do!
I decided to kind of mesh the movie-verse with comics verse; Natasha has the arc reactor, was kidnapped by terrorists in Afghanistan ad developed the Iron Woman etc in 2002. A couple of years later the Avengers thing happens, Steve is found in the ice, etc. Vague sequence of 616 events happens, though not everything because of the smaller time frame (I'm mostly just going to handwave this part aside from the effects they've had on Natasha's attitude - she's much more experienced than my Tony), and Natasha and Steve fall into a relationship that can be tempestuous but that makes them stronger in the end. They get married, and then we head back to the 616 timeline at the very beginning of Civil War. At which point they distract each other by presumably working out their aggression issues in the bedroom instead of through politics and Reed finishes his registration program and it works out for everyone. So! She's one of the leaders of the Avengers, married to Steve and running her company; Pepper and Happy are dating and Rhodey is still her college bff that she abuses. If you have any questions ask me!
The Kingdom Hearts trio is switching roles, and Kairi is going to be the angsty atoner who gave in to the Darkness! And now walks the path of twilight~
Hiroki and Nowaki are going to ~~high school au~~ it up. :D But their story is basically the same, they're just kids now.
Alice and Babs are staying normal I think.