Capcom confirms nothing is happening on the Marvel vs. Capcom 4 front, Niitsuma no longer in that division
Ryota Niitsuma, Marvel vs. Capcom 3's producer, stated that "nothing was happening on that front," in regards to a new entry in the franchise.
Not only that, but he'd been moved to a different division within Capcom.
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What logistical hurdles exist is anyone's guess, but we can speculate a bit based on past instances from Capcom.
Licensing has obviously been an issue, as Capcom doesn't fully control the rights to half of the cast members in the game.
This means Marvel requires some approval over the various aspects of these titles.
It's unlikely that this is the end of the Vs. series from Capcom, as these games have been a very strong success story for the company, but which flavor they'll take going forward is up for debate.
Source: Ryota Niitsuma's Twitter.