Retro has their own and looks like they maybe working on another just for Wii U for a new game. Better than Cry for Wii U just because it's made for the hardware instead of having to dial it up or down(Wii had a couple games in Unreal 3 even). Also Cry and Unreal are not good for every kind of game tho people seem to think slap Cry and Unreal on anything and wham bam.
Wii U can do Unreal 4 and hell even Unity a great middleware can produce some great looking games.http://unity3d.com/showcase/gallery
Just for Metroid it's better Retro/Nintendo use something custom for the Wii U itself. Not something they have to turn up or down esp when in MP3 all those environments were not cut and paste repeat but a lot of hand making it in the game. Nintendo can make it more there not using cry or unreal.
Devils Third is using unreal 3 right? I agree Retro would use an in-house engine.













