Mario and Luigi should most deifinitely be considered for Game of the Year. If more RPG's were like this, I'd play them more often, and probably wouldn't be so bitter toward them in general when I see one get egregiously high ranks from mags and sites (it's almost as if they are exempt from the review criteria.) The game is totally skill-based. Turn-based yes, but you can play through every dungeon and every (non-random) fight without receiving damage, if your reflexes are good enough. If you lose, it is your own fault, not some random dice-throw. You don't even have to level up if you don't want to. It makes it easier, but you can defeat every boss in the game at level 1. And the special attacks do more damage the better you get at performing them, and that is good game design. The unfortunate fact is this game will probably not be considered based on the fact that it didn't receive a lot of hype from magazines, and nobody considers the GBA a serious force.
For the GC, I am really torn between Wind Waker, Mario Kart, and F-Zero. F-Zero is for all consideration perfect. The gameplay is Fast and Furious(tm), the control is fantastic, and the track designs are insanely genius. With loads of unlockables, Arcade connectivity, Multiplayer, Online competition (Internet scoreboard, which is, for all intent and purpose, an online mode) it is hard to resist. It may be difficult, but it is not impossible.
MArio Kart is downright fun. I don't care what IGN says. I don't care what the haters say. It's fun. It's like a slower F-Zero GX with insane weapons and frantic action. And I have never seen a videogame so animated. Nothing in the game ever stops moving, the framerate never takes a dive. The Multiplayer is godly, Shine Theif on Tilt-a-Kart is a lovable chaos. Welcome addition, and good on ya Nintendo.
And of course, Wind Waker, which I think suffers in the mainstream's eye because it was released so early in the year, and those (people that would call Zelda something similar but starting with a "C") jerks, but the game remains fantastic to today. It is a beautiful work of art, with cool dungeons, WAY cool boss battles, and an enormous expansive world to explore and find things in at your leisure. "Great" is insufficient for this game.
What I think the GOTY is immaterial, but if I had to choose one or be dumped in pirahna-fill acid, I'd choose Wind Waker. I love it, it's so baaad.
Of course, I turned down many games when I thought of my picks, but are no less fantastic. Viewtiful Joe, Soul Calibur 2, FFTA, Fire Emblem, Wario ware and Advance Wars 2 all are superbly stellar titels which everybody can pick up and enjoy for the start. Sorry for the long post, heh.