I'd say the N64 did 3d polygons better sure, WAY better though... Eh. But that is to take out all aspects of story telling, which is what put gaming in the eye of mass audiences and made it what it is today. You really can't argue that. Now if you want to say Nintendo changed how games are played, I'm with you. But you wanna know who changed the way games are made?
On to the Wii U. It uses its own proprietary disks, so it's not really CD's it used. It doesn't play blu rays, but now we are kind of going outside of gaming. Memory was less, but you can also hook up external storage, so this wasn't really an issue. And yeah, not as strong as it's competitors, but could do (though granted to a lesser extent) everything the other consoles could do.
As for asymmetrical gaming, the reality is it was just too hard to develop. Nintendo bit off more than they could chew, and i can accept that when they not only had to dive in to HD gaming, but also have games playable across two screens, and it is a shame it never took off because it was awesome.
Oh I definitely would say the 3D polygon capabilities are way better.
Take a look at Coolboarders 3 vs 1080 Snowboarding. It ALMOST looks like a generational leap ahead. First you have actual shadows, the polygonal models are better, the resolution is much better. The only thing that the N64 didn't do as well was textures, but that was due to it's medium more than anything.
Regarding the Wii U, I meant optical discs when I said CD's, but my point is the same. The console wasn't nearly as innovative as the N64, neither on a hardware level or software level. The Wii U's big gimmick was never taken full advantage of, meanwhile the N64's helped propel gaming forward in a way that probably accelerated gaming a whole generation (By my estimates, analog sticks would have been implemented at the PS2 generation if Nintendo hadn't done it already with the N64). The N64 was the most innovative that propelled gaming forward, the most powerful, and had some of the highest rated games of the generation (Ocarina of Time at 99, THPS2 at 98, Perfect Dark at 97, Goldeneye at 96, Majoras Mask at 95, and Super Mario 64 at 94). The Wii U might have been the most innovative, but it wasn't the most powerful, it doesn't have nearly same highly lauded games (BotW at 97, Super Mario 3D World at 93, Smash Bros at 92...and that's it), and even it's innovations haven't propelled gaming forward in any significant way.
This is why the Wii U isn't as great as the N64.