Honestly, I think the SNES controller pad was the best and here's why:
Let me just say that I have all these systems and love playing games
on all of them, but I have come to the conclusion the SNES controller was the slickest, less annoying(for those who like the glass half full, half empty etc.), had the right amount of buttons for games, and most practical.
For example, the first NES controller I found did not have enough buttons. For those who love playing the Double Dragon and TMNT (Ninja Turtles) games, as I do and still love to, the combos were using UP + A or B(which for example was high punch or a jump kick), granted that's part of the challenge, but since we're controller pads, Mortal Kombat was a lot easier with a high kick and low kick buttons separately. And, yes, I know those are two separate game genres, but the idea is still sound lol.
While I love the N64 and Game Cube(and loved the Zelda games, don't we all?), the controller pads were similarly awkward(and honestly the game cube pad was better in this, and most, circumstances). The controllers for these two systems at times had too many buttons (and no not like a fun "too many" like on a Steve Morse album). I never used the L button, ever I don't recall, or really the directional pad, and, to my discredit, I'm not the near the greatest player at all and never will be, I might be the worst lol. I understand why the directional pad was there perhaps, maybe to get someone like me transitioned on the N64 and have an easier time doing so being the klutz that I can sometimes be lol. However, in contrast, like op89x said above, "I like the N64 because the Z-trigger felt the most natural" . I fully agree with this statement. I think the guys at Nintendo were a step closer to getting it perfect when they made the Z trigger button the way they did. And, by the way, I also agree with you op89x, with this statement "the C-buttons were always more precise than the Gamecube's C-stick." Right on the money with that one.
As far as the Wii goes, Its single handedly the greatest system to play as far as innovation with its new technology. I mean, I knew the Wii was going to be cool, but I never thought it would be EPIC. Like Motrax just said, Metroid Prime 3 works very well with the Wii controls("perhaps the best use of the controls so far" -GameSpy <I think lol), but when I just want to sack out after a hard days work, I resort to my older Nintendo systems(SNES in this case lol)or '''GASP''' my PS3. Granted, the best thing about this system is playing Wii Sports and getting a great workout, especially if you're playing boxing with the higher levels like the pro ones for long periods of time.
However, when it comes to classic games with slick graphics (in most cases), the controller being bland, cool colors, slick smoothed out pad(more specifically, the feel), just the right amount of buttons, and the most practical for the games and and technology of its time, I have to resort to my precious SNES. The only thing I found that I didn't like with the controller and games was that the games would use A and B, or Y and X for the same function. That's the only thing that was irritating sometimes. But, other than that, everything else was gravy. And, by the way, the SNES was not my first system (1st was NES), although if it was, I don't know if I would have enjoyed the NES as much as did and do now.
Too long too read I imagine!