Wilderness Lodge is an incredible place to stay! We got a free upgrade to Courtyard View, and my husband practically lived on the balcony the whole week. My kids loved the bunk beds, and not sharing a bed did make them sleep better. The place was beautiful -- we didn't go to the parks every day, and we had a great time at the pool, etc. Transportation was quite good, though it was rather crowded first thing in the morning. We'd go back to Wilderness Lodge in a heartbeat!
Having said that, our next stay will be at either the Dolphin or the Swan. Why? Because we plan to make Epcot and MGM major parts of our next trip, and transportation is easier from those locations. Also, I'm a teacher so I'll qualify for the discounts.
At what park(s) do you plan to spend most of your time? I'd let that guide your hotel decision.