Akuma being in MvsC3 is just a homage thing. He is the first Capcom character to crossover to a Marvel game, in which he was also a hidden character. (X-Men: Children of the Atom.... ugh hated using Silver Samurai)
X-23 is in because she is new and popular. I am glad Rogue is out honestly. I loved that Rogue but that Rogue doesn't exist anymore and to be honest I am not sure what they did with her after she was powerless or does she have Sunfire's powers.... Anyway Marvel got to pick who they wanted in the game for their side and they mentioned at Comic-con they wanted to add people that were popular and some that were uncommon.
I am shocked that Phoenix made it in. I know people love and miss Jean but it surprises me that they use this version of her since it isn't actually Jean Grey.
As for Trish, who else would they throw in from DMC? It looks like for some series they really wanted to have multiple people to represent. Virgil and what's his name from DMC 4 look to much like Dante, and I am glad they didn't go with Lady (really they couldn't come up with a better name) and Lucia (Ugh DMC2).
As much as I would love to see Powerstone in this I'm not shocked it isn't in the game. Capcom seems to over look this series alot. I mean would it really be that hard to release P.S.2 on the XB Live or PSN in HD with online Multiplayer.
I am shocked Rival Schools didn't make the cut. Really shocked.
Games like this will always have somebody we all think should had been in it. (Like ANY form of MegaMan, I mean I am getting desperate here I will even except Starforce at this point. I don't even like Starforce all that much.) All we can do is hope they show up later as DLC or in a sequel.