I've been trying to explain this to myself, and I've reached a conclusion that makes way too much sense:
Mr. Fantastic -> Dormammu -- explained through the Human Torch/Super-Skrull stuff
Emma Frost -> Phoenix -- telephatic female X-Men newcomers
Juggernaut -> Sentinel -- giant X-Men villain veterans
Shuma-Gorath -> M.O.D.O.K. -- obscure non-humanoid villains
Niitsuma mentioned wanting several Fantastic Four characters in the game, said that Emma Frost is his favorite X-Men character, and mentioned both Juggernaut and Shuma-Gorath as characters he proposed to Marvel. Elektra is the only character from the original leaked list that was neither hinted at nor mentioned by Niitsuma.
Incidentally, the only leaked list character without a sensible replacement match is Elektra -- and honestly, the only similarity she shares with Storm is her gender. One is a newcomer and the other is a veteran, and they're both from different series and have completely different play styles.
Besides, Storm is a really major character. Her exclusion would have meant a lot more than that of Dormammu, Phoenix, Sentinel, or M.O.D.O.K., and so it probably makes more sense that she was added to the roster entirely rather than replacing somebody else. From what we know, Frank West was removed from the game fairly late, and there wouldn't have been time to add a new character in his place. Because C.Viper is the only Capcom character missing from the list, she would have had to have been added later, and she'd need a Marvel counterpart to even the sides out -- Storm. Both characters were revealed together, too.
There's also the Hand Hideout stage. When most people think Hand, they think Daredevil and Elektra. Yes, Wolverine was associated with the Hand, but do you really think Capcom would have chosen that as an X-Men stage if they really wanted to include one, over the Danger Room, X-Mansion, Asteroid M, or Savage Land? The marqee series of the MvC franchise are Street Fighter and X-Men, and neither have stages. If Capcom intended for the Hand Hideout to be the X-Men stage, then that feeling of equality and comparability would be lost. Perhaps with DLC we'll see stages for Street Fighter and X-Men.