Wii, not even a contest. N64 is at the very bottom of my console preferences

N64 by far

Wii and it's not even close. Galaxy, Pikmin releases (the new play control versions are incredible), a decent RPG selection (no matter Xenoblade not being to my tastes), a big library with many good games.

N64 is the worst console Nintendo have ever put out. Nothing outside of 3D platformers, Snap and OOT - and none of its games have aged well at all (except Paper Mario and Pokemon Snap), they're pretty much all borderline unplayable today.

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.

How could I have forgotten Little King's Story, I loved that game. Another point in the Wii's favour. I hope they bring it or its Vita sequel to Switch

I think TTYD was better, but Super Paper Mario was excellent. I know it's not the turn-based RPG people wanted, but it's writing was impeccable and the gameplay was great, the 3D gimmick was actually really good. Easily my second favourite in the series.

It is StarFox 64. Just named differently in certain territory's for one reason or another.

Boy this is tough. I should compare these systems by hardware and software individually.

N64:

I loved the controllers, I loved that the console allows 4 controllers instantly and I thought the console's design was cool (much cooler than the boring grey brick called PS1). I also liked the design of the cartridges. Back then I didn't care if CDs were the better storage solution. I also didn't bother too much changing the peripherals into the controllers, though it did annoy me a little bit (I mean the Rumble Pak, Controller Pak and Transfer Pak). I loved the Rumble Pak!

Now the software was brilliant! Super Mario 64, Mario Kart 64, Smash Bros (me and my brother loved that one), Zelda OoT, Zelda MM (I'm one of those who like MM more than OoT), Starfox 64 (or Lylat Wars how PAL regions know it), Pokemon Snap, Pokemon Stadium, Excitebike 64, 1080° Snowboarding, Wave Race 64, Turok 1 and especially Turok 2, Extreme G 1+2, Yoshi's Story, F-Zero X,... And not to forget the amazing support that Rare put into the system with Banjo Kazooie, Banjo Tooie, Donkey Kong 64, Diddy Kong Racing, Jet Force Gemini (awesome game!), Goldeneye 64, Blast Corps...

Wii:

The console itself was slick, small, stylish. Perfect for me at the time since I was living in a small students' apartment with not too much space. I have so fond memories of chilling on my couch with my Wii, I had such a great time back then. The remote control design was a genious idea in my opinion. The motion controls were great and intuitive and I enjoyed them in many games. Some hardcore PS fans didn't understand the appeal, though. I remember showing SSX Blur to two friends back then from that camp and how a simple tilt of the nunchuck makes the character steer left and right, and they couldn't believe their eyes lol. I could almost literally hear their minds blow because they simply couldn't grasp that. What I didn't like though is the reliance on batteries. Back then the lithium ion batteries were not very common so Nintendo had to use normal batteries and I thought it was annoying to change them all the time. Wisely I only bought rechargables.

On the software side the Wii was also amazing! Super Mario Galaxy 1+2, Mario Kart Wii, Zelda TP, Zelda SS (I'm one of those who likes SS more than TP), Smash Bros. Brawl with its fantastic story mode, Metroid Prime 3, Metroid Other M (I'm one of those who appreciates that game no matter how stupid the story was), the extraordinarily great Xenoblade Chronicles, Sin & Punishment Star Successor, Pandora's Tower, Kirby's Adventure Wii, Kirby's Epic Yarn, No More Heroes 1+2, Project Zero 2, SSX Blur (this was the last EA game I ever purchased not because the game is bad but because EA), Donkey Kong Country Returns, Final Fantasy Crystal Chronicles: The Crystal Bearers (I can highly recommend that one), Super Paper Mario, and of course the absolute killer app of all time called Wii Sports. It's totally insane how much fun me and my brothers had with just the golf game alone.

*Sigh* Curl-6, why did you have to make me do this? I can't decide! Both are great both deserve to be the winners here, but ultimately, I shall pick the N64, the Wii! But it's ridiculously close.

It is difficult for me to compare those two systems with each other.

I loved both of the consoles and spent 1000 of hours on each of them.

That's a tough call. Both are amazing local multiplayer consoles in their own way. I think ultimately I'd go with N64 by a hair if only for the nostalgia/sentimentality. It's also tough to beat classics like Mario 64, Goldeneye, Mario Party, and all those Rare hits.. But Wii definitely wins in terms of its innovation and quantity of its library. 

Wii

Early 3d games have not aged well both regarding to graphics and controlls
Wii motion controlls
So many good wii games (also a lot of crap)