Neoxon is somewhat wrong... Marvel Contest of Champions came out December last year and it has both the X-Men and Fantastic Four represented. If there is a ban on X-Men and Fantastic Four, it would had to have happened this year at the earliest.
In any case, I would probably expect the X-Men and Fantastic Four characters to appear in a potential MvC4 mostly because there is a difference between making a throwaway mobile Marvel game without mutants and making the most well-known Marvel video game series have a sequel without mutants especially when most of what the series is known for comes from mutants. The former only gets X-Men & Fantastic Four fanboys pissed... The later gets gamers pissed off at you, and the last thing Marvel needs is gamers declaring them an enemy for leaving out Mag-freakin'-neto and Mango Sentinel and siding with Fox.
Now Marvel could get around it by having Avengers Vs. Capcom or Avengers Vs. Street Fighter, but that will raise questions about why it is a step back from Marvel Vs. Capcom 3 and lead back to the mutant issue. In fact, if there truly is a ban on using X-Men and Fantastic Four characters now, that would be the most likely reason why there isn't a Marvel Vs. Capcom 4 beyond Capcom's financial trouble. Marvel would know that gamers would crucify them if they forced Capcom to make a Marvel Vs. Capcom 4 without X-Men characters or Dr. Doom, so they don't allow one to be made.