Will we still see Mario Universe?

[F0X]

While it's true that EAD Tokyo has two development teams, one of them hasn't developed a game since Super Mario Galaxy. They might be focused on game engines or something.

At any rate, you're theory isn't quite based on fact. According to the Developer Direct, 3D World is indeed a direct sequel to 3D Land but was never going to be a 3DS game. The development team felt that their vision of 3D Mario multiplayer better served the Wii U, and I think they're right about that.