The regular rooms at the Wilderness Lodge and Animal Kingdom Lodge are the same size as the rooms at Caribbean Beach Resort, which is a moderate-priced resort.
There's a very big, very noticable difference in the room sizes of the AKL as compared to the Polynesian.
Having said that, I personally don't choose a resort based on room-size alone (unless DSs are with us). For just DH and I, the room at AKL was perfectly fine. How many people will be with you in your room??? That would make a big difference in whether you'd want to choose a larger room or not.