It's probably just help with making models etc, with directions from Sora of course, I don't think Namco will have much involvement with actually deciding gameplay elements, included characters, modes etc.
It's usually like this with most ninty collaborations, just like in the past with collaborations like Sega and F-Zero or Capcom and Zelda.
With minish cap for example the Zelda team still were the ones steering the development of that title, I don't expect this to be much different since it's a series Nintendo definitely wouldn't like to screw with.
This won't be another Other M scenario unless they for some reason gives Namco too much freedom, which they won't.
They made this decision since they need to put a lot more work into the graphics this time around. I'm expecting gameplay, style and music to be what Sakurai wants.
Judging by how competitive and complex Uprising was I'm expecting this game to be 10x better than Brawl, at least.
Especially now when Nintendo wants to have more titles with deep experiences than before, they've been saying this a lot lately and they have been saying that with Pikmin 3 too.
Brawl sucked and was casualized on purpose with slow paced fighting and stuff like tripping.