
According to the poster in the background of one of the new Ultimate Marvel vs Capcom 3 stages, all of the MvC2 characters that didn’t return to the game are labeled either Apprehended or Slain. Everyone except Mega Man, that is.
List of Apprehended Characters –
Colossus
Ruby Heart
Gambit
Hayato
Psylocke
BB Hood
Unknown?
List of Slain Characters –
Cyclops
Marrow
Ice Man
Jin Saotome
Cable
Amingo
Captain Commando
Son Son
Characters with no label or an obscured label –
Mega Man
Missing Characters –
Thanos
Blackheart
Venom
Juggernaut
Omega Red
Rogue
Sabretooth
Silver Samurai
Spiral
Anakaris
Roll
Servebot
Cammy
Charlie
Dan
Dhalsim
Guile
Ken
Bison
Sakura
Zangief