Eh, no. Mewtwo is more like how MegaMan is. A highly important character, but far less important than the main mascot. Especially considering Marvel VS Capcom started off via X-Men VS Street Fighter. Though of course, Mewtwo definitely is more important than MegaMan(in MVC) would be to Smash in comparison. MegaMan was given tons of praise for being in, but if he wasn't, it wouldn't make people too crazy to begin with. Some complaints, sure. When Mewtwo was cut, people were completely crazy over it. He wasn't in 4's base game, and it had a huge backlash. What saved the game was announcing him as DLC too.
It's why Pikachu is pretty much the Wolverine of the game. Mewtwo is more on MegaMan's level of importance. Absolutely should be in there, but clearly is not super high priority either. The fact they both have a "X" version is a coincidence... and not why I made the comparison either.
The other issue is that while people gave a lot of backlash to Mewtwo not being in Brawl, it still sold well because there was still a lot of great stuff. Part of why it's more like the MegaMan situation. If Pikachu wasn't in there? The game would do far more horribly. There's no way it wouldn't get immense backlash. Not even Mewtwo would be nearly as bad.
While MegaMan is definitely closer to Mewtwo when it comes to how important they are to MvC and Smash respectively, Pikachu is pretty much Smash's Wolverine. Removal of him is a death sentence for your game, or almost entirely. I haven't checked Infinite's sales, but I can definitely say it didn't do all that well from what I read. I think it still did decently enough due to people interested in mechanics, etc. at least.