Honestly, there aren't that many differences. They are located right across the lagoon from each other, so no matter which one you stay at, you'll have the convenience of location: you'll be able to walk to Epcot, walk to any of the restaurants, shops, arcades, etc. from either resort.
Also, the rooms are very similar in layout--only the theming is different.
The deciding factors may be prices of each resort, the theming, and the differences in pools (BCV has Stormalong Bay, a very large sand bottom pool and BWV has a more standard looking pool with a clown waterslide). Hope that helps!