The Gamecube controller was just another ok controller. I feel like that's the best we can hope for. It wasn't bad, but I didn't really enjoy it much. Didn't like the button setup. The C-stick nub was terrible, as was the Z button. The Analog stick was ok, had a good feel but I didn't like the top.
I don't like the PS3 or the Wii controllers. The PS3's buttons feel mushy and the "triggers" are awful. It also gives me hand cramps due to the shape. Not a big fan of the analog sticks, I prefer the 360's concave top and like a bit more resistance. The Wii is just an ergonomic nightmare to me (it needs the Classic which annoys me). Even for waving around I think it feels bad and trying to use it like a NES controller just makes you wish for the NES. I feel like the 360 is the best of the current ones but could be better. Obviously the d-pad, but the shoulder buttons feel awkward especially for games that use the triggers a lot (really wish they'd have put them on the underside of the controller).
I still wish Nintendo had really just put a second analog stick on the 3DS and made it the big controller for the Wii U.
Reasons:
Buttons logically laid out. There's a big fat *primary action* button, and then periphery action buttons
trigger buttons were a hybrid of analog and digital. They aren't concave like the PS3, are bigger than the xbox
analog stick seems to have a smaller dead zone and seems a bit more precise
The only great thing about that controller were the shoulder buttons. I remember Nintendo fanboys were going crazy because some Sega person claimed the Gamecube controller was so innovative it was going to completely change gaming. Turns out he was talking about the shoulder buttons ability to click like a button and be analog.
I personally loved the N64 controller the most... followed by the original xbox controller, the fat one... oh how I loved that thing! I never got used to the small one, but I really stopped playing console games at that point.
Zombie Andre the Giant? I actually did not hate the original Xbox controller. It takes getting used to but, I actually preferred it to the smaller one. The 360 is better than either though. I liked the N64, but it feels like such a toy and not in a good way (compared to like the NES controller which felt like a toy but in a good way).
Dreamcast controller
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I liked it at the time (and think a new one with a space to slide like an iPhone like its a giant VMU would be pretty cool, Ikaruga would be great), but was a bit too cheap feeling. I liked the shape (I really like that sorta handle feeling it and the Gamecube had on "wings"), but the buttons weren't very good. I actually did kinda like the analog stick but it wasn't great either. Triggers were ok.
The VMU was a great idea probably 10 years ahead of its time. Sega should take that idea and make it an app.