Since the location is pretty much the same (EPCOT resorts-use same transportation), I would base my decision on a few factors.
The 2 bedroom villas are really nice! You would have a full kitchen if you intend to use it, it could save some $$$. Plus, you also have a washer and dryer, so you could pack lighter. Also on top of the kitchen and washer/dryer, the 2 bedroom villa will give you a master suite w/jacuzzi tub big enough for 2

, 2nd bathroom, living room, dining table, 2nd bedroom w/either 2 queens or a queen and sleeper, real dishes, dishwasher, microwave, toaster, sleeper couch in the living room, access to Storm along Bay (nicest pool on property) and 3 exits to a balcony. Sorry, but I probably missed some of the extras. Hopefully someone picks up where I left off.
It is totally different than getting a hotel room/suite. It is like having a small fully functional home at WDW. I have stayed at the BCV and really enjoyed them. They are not my favorite of the Home away from homes, but they are very nice.
I have not stayed at the Swan/Dolphin yet, but we have walked through there many times while staying at the BWV. They are very attractive resorts.
We are staying at the Swan/Dolphin along w/the VWL and BWV during our 3 week stay and I am excited to try out either the Swan or Dolphin. I think it will be a perfect mix!
IMO-If you wouldn't use the ammenities in the room at BCV, then I don't see any point in paying for them. Some will argue BCV has more of a theme than the Swan/Dolphin, but they are both deluxe accomodations. So for me, that would not sway me.
Personally if money were no big object, I would choose the 2 bedroom. I love having 3 separate living areas to spread out into. I let the kids sleep/hang out in the 2nd bedroom, and when they go to bed, my husband and I still have the living area, kitchen, master bedroom and bath to relax in. We also eat breakfast everyday and usually lunch or dinner in our room, so we save money on food by eating only 1 meal out/day. I also make use of the washer/dryer.
We LOVE the home away from home resorts so much that we bought into the DVC

We have stayed in all the WDW DVC resorts, and enjoyed all of them.
I am sure you will get more info/opinions from others. I hope they make your decision easier.