We have stayed at both. The Vistana Villages units are newer, and a smaller resort in comparison to the Vistana Resort.
My family prefers the Vistana Resort because of the activities. We have stayed here a few times and just hung at at the resort. LOTS of activities for the kids (big and small). You could pool hop to a different pool each day. The summer time is the best. Also, we have found the staff at the VR to be more friendly and the maintenance much better.
Either location (VV or VR) is great for access to Disney parks.