Marvel is intentionally deemphasizing the FF and mutants.
uhhh you do realize that Marvel is currently in the middle of a huge X-Men push that involves launching FIVE new team books (X-Men Blue, X-Men Gold, Astonishing X-Men, Weapon X, and Generation X) as well as 3 new solo books (Cable, Jean Grey, and Iceman). Blue and Gold are even twice-a-month books!
Also Marvel Heroes Omega launched on PS4 earlier this year, with a dozen playable X-Men characters. No FF though, you're right about that.
They aren't de-emphasizing mutants at all anymore. It's possible they still were when the licensing contracts for Infinite were being written, though. Or maybe they only want them to be DLC for financial reasons, like if Fox gets a cut of the sales for stuff with X-Men in it, they'd rather only give a cut of the $5 DLC downloads and not the $60 base game.
Man it boggles my mind that people still try to defend that no, Marvel's totally 100% supporting the X-Men! Like, ignore that they were left out of Disney Infinity, Lego Marvel Super Heroes 2 and now Marvel v. Capcom as well? ---
