VWL isn't my favorite resort, but we did enjoy ourselves there.
I had mixed feelings about the transportation. Loved the boats to MK -- and also the boat over to the Contemporary that allows you to enjoy the restaurants there or hop a Monorail to Poly & GF. Didn't like being diverted through Fort Wilderness on the bus routes, though. I will say that the location of the bus stop is very convenient to the villas at Wilderness Lodge. (It's a bit of a hike at the BWV. And now that I think about it, the bus route at the Boardwalk is my all-time most disliked. I'm to the point where we probably won't stay at an Epcot resort again without a car.)
I'm personally not big on balcony sitting, so the view (trees, trees, and more trees) at VWL didn't impact me that much. I know some people really judge a resort by its views, and many are disappointed with this aspect of VWL.
You can't beat the location of the villas for quick access to the main lobby and the pools, though. Ask for a room near the elevator and you're literally out your door and right in the lobby. WL's lobby is so beautiful -- especially at Christmas. I also enjoy relaxing in the Iron Spike Room -- or whatever they're calling it these days.
Although the 2-bdrm villas at VWL are actually 13 sq ft larger than those at the Boardwalk, the color schemes make a big difference in how the size of the rooms "feel." Had I not just looked it up to verify, I would have sworn to you that VWL had the smaller units of the two. The dark greens and dark stained woods make the rooms feel smaller, while the bright pastel rooms and light furniture at the BWV make those rooms seem larger.
There's no evil clown at the Wilderness Lodge. They have that going for them. Although I would say the slide is better (theme aside) at the Boardwalk.
BWV has the Boardwalk, it's attractions and performers. VWL gets the Electrical Water Pageant.