Katsuhiro Harada stated the below about how he is going to be involved in the development process of Super Smash Bros. for the Wii U and 3DS:

“Although we’ll help provide support on technology and other things involved creating the game, I’m currently very focused on the Tekken series. Some people might say online that I’m going to be involved in the development process or not but that shouldn’t really be an issue because the game design is going to be handled [by] Masahiro Sakurai. So I don’t understand why there would be any worries there.”

Harada is stating here that there is really no need to worry about Namco Bandai entering in with the development of Super Smash Bros. since Masahiro Sakurai is still in charge of the game’s design. If Namco Bandai has an idea for the game that they want to implement then I think they would have to go through him to approve it.

Source: mynintendonews.com