According to our sources, Capcom will make a Capcom vs. Namco game using the Street Fighter IV engine and Namco Bandai will create Namco vs. Capcom with the Tekken 6 engine. This means that each game will play and look like whichever company is creating it. Think hadoukens, Ultra Combos, and 2.5D presentation on the Capcom side and three dimensional movement, in-depth move lists, and most likely, a playable panda on the Namco side. Ono is rumored to produce the Capcom game, and we're guessing that Harada will handle the Namco end of things.
Note these are fighting games, not a continuation of the old Namco x Cappcom RPG title that appeared on the previous hardware generation. Why two games? Simple: each company makes one! Capcom would be developing Capcom vs Namco, built on the Street Fighter IV engine, while Namco will develop Namco vs Capcom, which will run on the Tekken 6 engine.
As fighting game fans are already no doubt coming to grips with, this would mean two significantly different games, Street Fighter IV's 2D arenas contrasted nicely with Tekken's more three-dimensional combat.
GI say that Street Fighter IV producer Yoshinori Ono is handling Capcom's side of the deal, while it's expected Namco Bandai's Katsuhiro Harada will be in charge of the opposing project.