Ya know, I’ve sorta wondered the same thing myself. They did Namco x Capcom with… err… Capcom, but it wasn’t a fighting game. Instead they did a crossover with Tekken. IMHO, I think Namco Bandai didn’t do a manga fighting crossover, because Capcom did that with Takara Tomy (Tatsunoko vs. Capcom), who is an old rival of Namco Bandai. Or maybe it was Capcom who didn’t want to get Takara Tomy angry and make a better game with Namco Bandai, than they did with them.
Then again, it’s not like Namco Bandai needs Capcom to make fighting games… so it’s probably just more of Namco Bandai’s weird off-and-on stupidity showing again.
Hmm… they should make an Idolmaster fighting game.
EDIT
Now that I really think about it. When you look at ALL the IP’s that Namco Bandai owns or has merchandising rights to… it’s a LOT of iconic or mega popular series. Freak’in insane.