I think the N64 had many more great masterpieces while the GC has many... okay... games.
I can't stand ED as a game, good story through, the RE series are just remakes (of remakes, of remakes, of remakes, of remakes).
Mario, Mario Kart, Zelda, Star Fox all much better on the N64.
The N64 had masterpieces of games, like Goldemeye and Mario 64 which were / are used as a basic for FPS and 3D platformers.
The difference is that the GC had like 3 times as many games, so it has many good/great games, and many others that were at least playable. On the other hand the N64 had fewer games, but the good/great games were amazing.
I'm a huge fan of Crusis'n USA and World. Goldeneye and Perfect Dark, there is Super Smash Bros, and in japan Animal Crossing that are great and turned into franchises. Mario Kart 64 is great while the GC one is ehh at best. Plus the third party games were okay a lot of the time too, Star Wars Racer, Shadowman, and The New Tetris.
I think all Nintendo systems have their high points. The n64's high points were first party games while with the GC it is not the well know huge franchises.