Do both! Make MM for the Wii u and LTTP for 3DS. Problem solved.
I can top that.
Majora's Mask 3DS developed by Grezzo (seeing as how you know, Ocarina of Time, take same code, blah blah blah), and LTTP developed by Shigeru's team seeing as how he wants to do it and put it on 3DS as well. Shit, they do it for Pokemon. Do it again like they did with Oracle of Seasons/Time by releasing them at the same time. (that might be a bit far but still).
Or just make MM on 3DS and put LTTP on downloadable shop title on WiiU or vice versa.