A 2D Metroid game from Retro doesn't seem very likely, sadly enough. 2D Metroid is mostly handled by SPD 1 because of Sakomoto's presence, while the relationship with Retro is handled by SPD 3. On the other hand, Sakomoto is division leader now, so... I don't know: you can always hope. If Retro were to make another Metroid game it would probably be a Prime game, but most likely the next Prime will be made by Next Level Games and they're still finishing up that Federation Force game.
With regards to Paper Mario, that one is handled by SPD 3 and Intelligent Systems. Intelligent Systems has been very bussy, so I'm not sure they have enough people left to finish a Paper Mario game for WiiU. I'm hoping to see this one as well, as much as you are, but I'm doubtful it will happen.
But what are we gonna have for Wii U in 2016 and 2017?