N64, I would pick Kirby over Metroid any day
Mario 64 vs Mario Sunshine
Ocarina of Time + Majora's Mask vs Wind Waker and Twilight Princess
Kirby 64 vs Kirby Air Ride
Star Fox 64 vs Star Fox Adventures
Super Smash Bros vs Smash Bros Melee
Mario Kart 64 vs Double Dash
Both had their fair share of great new ip's, but I perfer N64's
N64
Banjo-Kazooie
Conker's Bad Fur Day
Perfect Dark
Animal Crossing (jp only, later ported to gamecube)
Smash Bros
GC
Pikmin
Viewtiful Joe
All I can think of :/