To Nintendo's credit, there is one franchise that still captures my heart more than anything Mario-related. Not Donkey Kong or Metroid. Not the Smash Bros series. It is The Legend of Zelda series. I actually didn't like it at all until Twilight Princess. That game felt more epic and nicer to look at than Ocarina of Time and Wind Waker. To me, that is Nintendo's Final Fantasy series for me. It can feel boring and tedious trying to figure your way out of the dungeon, but the boss fights were amazing like in Sony's God of War series. I wasn't really a believer in Link until Twilight Princess. I grew bored playing the 8-bit and 16-bit classics.
I always felt Mario was better done in 2D. I liked Super Mario 64 but I didn't love it like Super Mario Bros 1-3 and World. I think Link's world is better for 3D while Mario and Sonic should stick to 2D. That is the genre Nintendo is the master at thanks to the brilliance of Miyamoto. Platform games and inspiring the kart racing copycats. And I would love to see Nintendo release Mike Tyson's PunchOut!! to us. No ROM. Just an official release of that 80's classic with no retouches. That was one of the most perfect games that doesn't need a graphical remake. Epic music with epic gameplay. Mr. Sandman is the one that always gave me hell.
http://www.youtube.com/watch?v=mfEOHcGFchY