The art and character designs.
That point right there you have already alienated a bunch of people who might be interested mechanically in the game.
Once you managed to hook someone in based on the allure of the team mechanics... then you had to deal with vanilla Skullgirls which was a mess. The IPS kept changing and even then originally you had long combos and just some weird shit with it. It was really hard to keep up with so many iterations on those changes. It's good now but it was a lot asking people to stick around for over a year before these problems were fixed.
Next problem is that initially and arguably still to this day... Skullgirls simply does not have the character roster size to accommodate for a potential 3v3 fighter. If you have like 9 characters starting out and you need to build a team of 3... well you are using 1/3rd of the cast on your team already! Being able to use any move for an assist is an excellent feature that Enzo will come in and berate on but he's wrong and should not be catered to... but the issue is that the best move for an assist generally gets figured out and you will still end up with the same few team configurations that work. So you still need a lot of characters for this to work well.
The character ratio system is also something that is debatable. I personally like it but for others it might not be very appealing. When you first get into the game you think "man I should just concentrate on one character and play a solo character" and then you get locked into a single character not willing to try out a multi character team. It's one of those things that is better to pick one option rather than have the user be able to use all possible options. It's both a strength and a weakness of the game.
The other problems are more minor but they are still substantial to talk about when framed in the context of a MVC2 successor. The game is 6 buttons but assists require you to press two buttons. The game is trying to be SF-esque with its button lay outs but it has a lot of other double button inputs for stuff like throws and assists. The appeal of a game like MVC2 is that you have easy one button throws and one button assists. It's a complexity issue that sort of pushes away newcomers (and Skullgirls has enough of that as it is). MVC2/MVC3 are definitely not newcomer friendly but starting out it's easier to grasp into the 4 attack buttons and two assist buttons. It's easy to air throw people and call assists which feed into the fast paced, team based play style of the game.
Another smaller issue is that the game doesn't really emulate the pace and structure of MVC2/MVC3. I am not talking just about the speed here (Skullgirls is fast but not as fast) but rather the verticality of the action. Super jumping is kinda limited in Skullgirls as is aerial mobility for most of the cast (Painwheel is really the closest to an aerial character in Skullgirls) so that focuses most of the combat on the ground. MVC3 did this as well a bit compared to MVC2 but a lot of the action was still in the air with characters with really fast dashes and flights. This structuring of the action is what really separates the Marvel games from many other anime games combined with the team based game play (which to be fair Skullgirls does emulate well).
Skullgirls is one of the closest games to MVC2/MVC3 but it's still not a "Mahvel" game (and I am not talking about Marvel characters here obviously). Mike Z can call it MVC2-like as much as he wants but it doesn't hit the same notes as that game does.
Edit: Fucking Zissou beat me to it god damn it. He pretty much said what I said here.
