For me it's the fact that 2D platformers are a dime a dozen these days, and in my opinion Nintendo isn't even making the best ones anymore. (My favourite these past years is Rayman Legends).
I bought and played Donkey Kong Returns on Wii, and although it was a fun game I frankly found it way too frustrating. Maybe I suck at 2D games, but Legends shows us there is a better way to make a game challenging than limiting lives and having few checkpoints.
Meaning: Give checkpoints all the f***** time. A challenge doesn't become more rewarding if you have to do parts that you've already mastered again. And lives are a thing of the past.
The second part is the fact that Wii U still really needs a killer app. Retro could be the studio to deliver that, and another Donkey Kong is not what Nintendo needs right now.
An epic, full scale beatiful looking game that utilizes the Gamepad in exciting ways is what is needed, sooner rather than later.This could EASILY be a new Metroid Prime (the Wii U Gamepad almost seems to be made for scanning stuff), or retro could make a totally new IP.
So yeah. It also worries me somewhat that a 2D platformer together with a problebably iterary (although awesome) Super Smash is supposed to save Wii U's ass in 2014. I have my doubts.
We shouldn't draw conclusions though. Maybe Retro only devotes a smaller team to Donkey, and is in secret developing another game. Maybe they've expanded.