There is a difference. I have never visited the Villages, but it is a smaller, newer resort. You will not find as many amenities as you will on the larger Vistana resort, namely no onsite restaurants, but there is a poolside bar. Also one pool at the Villages vs 7 at the main resort.
I've heard only very positive things about the Villages. The villas are all new and very nice from what I've read and been told. I do believe if you are staying at the Villages you can drive over and use the facilities at the main resort ? Not sure if this is still true, but it was like this last time I heard.