Going by games made for the system, I'd favour the N64. Super Mario 64, Goldeneye, Ocarina of Time, Banjo Kazooie and Donkey Kong 64 really grabbed me at the time, and I still enjoy all of them to this day. Silicon Valley and Beetle Adventure Racing are two of my favourite 'hidden gem' style games as well. From memory, only Super Mario Galaxy really had that sort of effect for me on the Wii. Skyward Sword was also a big let down in my eyes. However, experiencing the consoles at different times in my life will have had an effect. I was younger and had far less responsibilities in the N64 era, whereas I was busier and couldn't really dig into the games available for the Wii.

Wii of course has the Virtual Console and backwards compatibility, both major pluses. Not a huge fan of the motion controls though.

Wii by a lot. Bigger games library, overall cheaper (games). Got an online Mario Kart. Virtual Console where you could also play some N64 games.

N64 has aged really bad imo.

Library wise Wii while N64 had some defining games for 3D gaming it still lacks in library overall it's just that it's stand out games were industry shaking.

N64 by far. I agree the N64 didn't age well, but I had way more fun with it. My age at the N64 (13+) playes a big part in it of course, compared to my age with the Wii (23+).

Zelda OoT still feels as the best game ever. None other Zelda game since then came even close.
Goldeneye's singleplayer and multiplayer were really fun. Back then you still played with friends in the same room ;)
Perfect Dark looked so beautifull the first time I played it and the extra missions were just a game by itself. Multiplayer was really good.
ISS 98 Probably the game I played most in my life.
F-Zero Could play that game again and again. The steps in difficult level were really good.
Wave Race, Almost as good as F-Zero
Starfox 64 Again a game which I could play again and again.
The Star wars roque squadron games. Loved those
I played paper mario years later, but that one was really fun as well. Although it was my first and only paper mario as Zelda OoT was my first Zelda.

Besides these games I still played at least 10 more which were at least an 8 for me.

Wii
Mario Galaxy 1. Best Mario Ever. Liked it a lot more than Mario64
Resident Evil 4 Extremely good, and the controls (after i got used to it) worked really well.

Didn't play Xenoblade. But I guess this is the list I have really good memories of for the Wii ;)

N64 was around that time that gaming didn't really interest me that much, I think Wii wins because of that. Not to say the few games i played on N64 were bad, the Zeldas for instance are better in N64 than Wii.

Easily Wii simply because it has more notable games. The Wii has games I can still enjoy playing now, I don't feel that way about many N64 games.

N64's significance is mostly nostalgic. That was a time when major innovation was happening in 3D gaming, but innovation and great games aren't the always the same thing. Not much of the N64 era aged well.

I look at the 7th gen as period where developers really learned from past generations and started creating much more refined and balanced games. The Wii is part of that generation. Notable Wii games have and will continue to age better.

Honestly, I'd take Wii U over N64 as well for the same reasons. More notable and refined content. But neither Wii or Wii U or were around while developers were creating innovative content on N64.

N64. No contest.

N64 near the top

Wii near the bottom

I mean. I wouldn't be against the idea of a StarFox RTS in the same vein as Halo Wars. Seriously.

Wii had a ton of classics too and it could play GameCube games and others as well, therefore it gets my vote.