I can see an appreciable difference between GC and the Wii, but it's not major enough to make me think that GC games look awful. Everything is definitely more refined.
I really can't see how the controls for most games are bad. I'd argue more that the controller is what's bad (mainly the joy stick for being really obnoxious). But I have never had an issue with any of the control schemes. Mario 64 had very good controls. Zelda played fine. Kirby 64 played fine. Bomberman did too. Mario Spin Offs, Banjo Kazooie games, even shooters played fine. The issue was never with the control schemes, but more so with the joystick being really loose and having really low sensitivity.
The graphics really don't make anything unplayable, either. I've never played RE2, but I really haven't ever had any trouble identifying what I was doing the entire time I've played games on the N64. Everything looks pretty clunky, but it's definitely not a cluster**** of shapes that are impossible to decipher.
I'd argue that the major titles actually do still have an ability to contend with their counterparts. Taking the Mario series, for example. Mario 64 is a totally different game than Sunshine, which is still completely different from Galaxy, and even Galaxy is different than Galaxy 2. They each have completely differeny styles. Mario 64 had a lot of exploration and non-linearity. Sunshine was somewhat more linear, but it had FLUDD and some neat little Shine challenges (Red Coins, the hidden areas without FLUDD, etc.) Galaxy was HUGE. Galaxy 2 was more linear and more of a straightforward platformer, but that's still a different premise than each of the major titles before it. I play different games in the series depending on what I'm in the mood for. I definitely play 64 more than Galaxy, that's for sure.