I'd like to see Doc Ock, if the new trilogy is not going to be using him. We got pretty close in EoT, but still no dice.
Sandman should be out. Honestly, Beenox did all it could do with him in SD. Anything after his conceptually impressive level would feel like a disappointment. Have Hydro-Man take his place instead. We have never seen him in a game before.
Since we've getting the Spider-Slayers, how about Spencer or Allistair Smythe. The latter especially could be interesting, since they can use his Ultimate form or his newest Slayer armor for a boss fight. And if the new movie trilogy won't be interested in crime lords, how about introducing a few rival gangs? If they can't get Kingpin, then they could use Tombstone as the Big Man or Mr. Negative.