There are a lot of problems with supporting two distinct libraries. Every team of every major Nintendo IP is now going to have to make two distinct games for each of the big IPs.
That means the 3D Mario team (EAD Tokyo) has to make Mario Galaxy 3 and then Mario Galaxy 4, one for the portable and then one for the console. Or 3D Land/3D World.
Same with Splatoon. Same with Animal Crossing (unless the console is a flop, which isn't a good problem to have), Same with 3D Zelda etc. etc. etc. This means Nintendo teams are basically stuck working on the same IP for 4-5 years straight.
Unifying the library has bigger advantages than just helping Nintendo, they can now actually just make one Mario Kart for example and the team might be able to work on a different Nintendo IP (like Wave Race, that would be fucking nice after almost 15 bloody years off) or maybe (gasp!) work on something new.
I just don't see the benefit of continuing on, and I don't think Nintendo can do it either. "Nintendo is super efficient!" ... is one thing (actually they're really not as almost every major Wii U title has suffered long delays with their really big scale HD titles Xenoblade and Zelda U being in development for over 3 years each) but expecting them to be able to support two high end consoles simultaneously is bordering on insanity in my opinion.
It's just not doable they can't really even support the Wii U and 3DS simultaneously as is, the jump from 3DS (GCN/PS2 graphics) to XB360 level is immense too. When you get to that level of 3D the scope of the games becomes so much bigger and the visual fidelity becomes so much better.
I'll take unified library. Besides spending $500-$600 on two pieces of hardware just to play all the Nintendo games may be something Nintendo fanatics think is a great setup but guess what .... the vast majority of the market, even those who buy Nintendo hardware disagree. Most GBA buyers did not buy a GameCube, and most 3DS buyers aren't touching the Wii U, Wii needed the most revolutionary controller in the history of the business.







