The main complaints seem to be the character choices for the roster. People seem to have just wanted this to be MVC2.5. Combine someone who just bases everything off a cartoon from the 90s with a narrow mind and there's the problem. They think that only characters THEY'VE been exposed to should be in.
If the Marvel side is really the result of Marvel meddling, then I hope they continue doing it. Because if the general public always had their way, every Marvel game would consist of Wolverine, Cyclops, Storm, Iceman, Psylocke, Rogue, Gambit, Cable, Nightcrawler, Magneto, Juggernaut, Sabretooth, Spider-man, Venom, Carnage, Deadpool, Cap, Hulk, Iron Man, Thor, Blade, Punisher, Doom, and the F4. It would just be the same roster over and over and over again. We'd barely get any newcomers and classic characters like Hawkeye, Strange, and Iron Fist never would have gotten a chance to shine.
As for the Capcom side, it would be filled to SF characters, because people don't realize that there's more to Capcom than just that and that they've been in plenty of FG, whereas other Capcom characters don't get many chances to be in a FG. Not to mention they already have a crossover with Tekken coming out. Their excuse is usually "We wouldn't have MVC if it wasn't for SF" or "SF started the vs series so they should have more characters". This doesn't mean that everything time a vs game comes, they should have a bunch of SFer's in our faces.