If that's what you would prefer, go for it. I had already been going for the PC version and once I played Morrowind on PC, I knew TES games were best for me on the PC. You can still use a 360 controller and even get a PS3 controller working on the PC. Both controllers will work for Skyrim. I prefer keyboard and mouse, but my preferred console controller next to the Gamecube one(dem buttons are so fun to look at) is any of the Playstation brand ones. The layout is perfect for my hands.
I have used a 360 controller on 360s before, but found the controller confusing. Despite the fact that it is like a Dreamcast controller, which is something I could understand easier... I blame the fact that I was playing Black Ops just because that was what was in the cousins 360. I am used to how PS3 controls are in shooters.