M.O.D.O.K. was suggested by Marvel themselves if I remember correctly. He is a major villain of the Marvel Universe and adds an extremely different type of playstyle to the table, which I think is far more important than just being a lot of characters who are only considered "cool" but play completely alike. If it went like the fans want, we'd have Venom and Carnage along with Spider-Man... woohoo clones much?
In any case...
I'm gonna give you the facts regarding the DLC and the characters outside of the original 37 (including Galactus) available in the getgo-version.
Jill is not finished. She lacks quite a lot of stuff - sound files, challenge data, balance.
Shuma-Gorath is pretty much 100% finished, but he was postponed because Marvel didn't want him to be on the starting roster.
Frank West and Doctor Octopus both have been scrapped, there's only folders containing their names, however, there's no data left regarding them - no textures, models, sound, not even a fraction of data.
Frank West is confirmed to have been worked on by the developers, but got scrapped later on, while Doc Ock was very likely to have been intended to be included but at some point of the development, he was dropped.
Aside from an incomplete Jill and a finished Shuma-Gorath, though, nothing is on the disc.
My guess is that Shuma-Gorath and Frank were supposed to be available in the starting roster, and Jill and Doctor Octopus were supposed to be the first pair of DLC characters. However, since Frank's moves were so weird, they realized they couldn't finish him on time (see the fuzz about him being cut), so they started working on Jill instead. I guess both the deadline and Marvel saying no to Shuma-Gorath on the starting roster was reason why these two didn't make the cut.
Additionally to that, I'm fine with them being on the disc already, there are reasons behind it - Jill isn't finished and Shuma-Gorath was supposed to be in but Marvel refused to accept that. So this time it wasn't just plain squeezing the money out of your wallet like they did with the stupid alternate costumes in SF4 and SSF4. Also, speaking of which, I think there's only like 5 alt costume sets on the disc for MvC3.