We stayed at CSR in 2007 and WL in 2006. If I had a choice, I would pick WL.
For us, there is something very magical about staying so close to MK. I remember being in the pool at WL and suddenly looking up at the lodge towering over me and I felt so lucky to be there. The lodge is beautiful. We enjoyed the ease of getting to Mk by bus or boat. We liked being picked up and dropped off at one spot outside the lodge and enjoyed the interior corridors, especially at night. And believe it or not, we preferred Roaring Fork over Pepper Market. We got waited on a lot faster at WL. They didn't try to ignore you (like we found at PM) and they were just nicer, in our experience, anyway. Transportation was pretty good.
We also enjoyed our stay at CSR. It is a very pretty resort. The pool is larger than WL's pool, thus it never felt crowded, and you could always find a lounge chair at CSR (unlike WL, which I felt, may have had their share of pool hoppers). The bus service was top notch, in our experience. CSR is in a pretty good central location. It never seemed to take long to get to any of the parks. Loved the bright decor and all the pretty fountains.
The two are very different in looks. I would stay at either one again in a heartbeat, but I think WL has an overall edge over CSR after our stays at both.