Wii is my favorite console of all time. Any console would lose when put next to it. But with the comparisons:
Mario 64 vs the Galaxy games: No contest the Galaxy games. Mario 64 is still good, but Galaxy 1 and 2 are the best Mario games ever.
Ocarina and Majora vs Twilight Princess and Skyward Sword. I first played Ocarina and Twilight Princess at the same time, and Twilight Princess was much better in every way. And Skyward Sword is my favorite videogame of all time.
Smash 64 vs Brawl. Yeah, 1 has little content and the other is overflowing with content. Not even fair.
DK64 vs Donkey Kong Country Returns. Retro beats Rare here.
Paper Mario vs Super Paper Mario and 3 Mario parties each. Really the only matchups where the N64 version wins.
Shooters: Pointer controls vs single-analog stick controls. No contest the best Wii shooters beat the best N64 shooters.
N64 had Star Fox, F-Zero, Banjo, Conker. Wii had Metroid, Wii Sports, Exite, Xenoblade, Epic Mickey, Sonic Colors. Definitely prefer the Wii offerings.