I was playing some more Donkey Kong Country Returns again rcently and, you know what?
I think the big secret game Retro is working on is DKC 3DS.
I base my speculation on the fact there is so much gameplay in DKCR that takes place on more than one plane. You are often barreling into the background, kind've like in Mutant Mudds. So, I think Retro's DK easily lends itself to further gameplay on the 3DS. It'd be, I suppose, relatively easy for them to do, too. They have the art assets and gameplay engine and whatnot already. They probably have leftover level ideas too, just like the Mario Galaxy team did, which led nicely into Galaxy 2.
(p.s., why is this in the WiiU thread? Well, folk have been a-speculating what Retro is up to and also everyone's been talking about Metroid. Made me think of this).