Well, despite wide spread claims that the games framerate is worse than the N64 version I haven't had any problems. In fact I haven't noticed any slow down other than at the first cinema scene where Navi flies to Link's tree house. It paused for a very very brief time other wise I haven't had any problems. Of course I'm only up to Jabu Jabu so I haven't been in any areas were there are a ton of enemies at once. Also slow down has never really bothered me that much unless it is severe and frequent so I may just not be noticing it when it happens.
As far as the graphics go it's kind of a mixed bag. Because of the higher resolution detailed models look better (sharper, brighter, and smoother) but things that are less detailed like the 2D sprites used for items, bushes, and some of the scenery look worse. It's really not a big deal though. First of all unless you are a graphics freak it shouldn't bother you and the games graphics are outdated period. Besides what the better resolution pretties up out weighs what it makes ugly. As an example do you remember that little drawing that Link had at the bottom of his tree house. Well, on the N64 version it was kind of hard to make out what it was supposed to be but now you can easily tell what it is even from a distance (I mean like a few feet away since in the N64 version you had to be right up against it in first person view to tell what it was).
As far as the controls go I was really worried when I first started playing the game. I was having a real hard time controlling Link but this was probably due more so than anything to the fact I hadn't played the game in like two years. Anyway by the time I got done with the Deku Tree dungeon I was already getting used to them. It's also very nice getting to play the game on the GameCube controller. Some people feel that the N64 is superior to the GameCube controller but I don't agree. For one thing it's more comfortable and natural to hold and it's nicer controlling Link with a analog stick that has more tension, is shorter, fatter, and has rubber on it.
I was also worried about using the C-stick instead of buttons but it's just as easy if not easier than the C-buttons on the N64 controller. Although you can use the Z trigger, Y, and X button instead of the C-stick it's more comfortable using the C-stick. Also one thing that is neat about the using the C-stick with the slingshot and bow & arrow is when you set them to C-down and push down on the C-stick to fire the weapon in first person it's like you are pulling back on the string. Well sorta.