We own BWV so perhaps are biased. Absolutely agree that Stormalong Bay at the Yacht & Beach Club is the best pool on-property, but Luna Park at the Boardwalk is very nice and I prefer the slide there because my kids don't have to leave the pool area to access the slide, unlike at SAB where they have to cut across the walkway going around the lagoon. This may not be an issue for you if you don't have kids or plan on using the pools.
Other than SAB, I give the nod to BWV (and we have also stayed at the Beach Club). If you're only interested in Epcot, then of course BCV are closest. If, however, you split time between Epcot and DHS like we do, then you may really appreciate the relatively short walk along the canal to DHS, and you are still pretty close to Epcot + you can use the Friendship boats which always make their first and last stop at the Boardwalk prior to leaving from or heading to Epcot.
And in terms of CS dining options, besides the Luna Park pool which does offer limited lunch items like sandwiches, the Boardwalk Bakery offers breakfast sandwiches (in addition to muffins, etc.) but also lunch sandwiches and salads. The Bellevue Room in the hotel side offers continental breakfast in the morning and becomes a bar in the afternoon/evening. And there are several 'food carts' on the Boardwalk where you can get hot dogs, etc. And you can get appetizers at the ESPN Club bar rather than a full meal.
Except for one small corner of the BWV exterior facing the Boardwalk, you can actually stay under cover while walking to the Flying Fish (first restaurant as you make the turn toward Epcot) and then the Flying Fish is connected to Seashore Sweets and Spoodles so you can get to these places without getting rained on.
As far as the rehab goes, they are doing both interior and exterior work but the two projects are not related -- meaning where they are doing the exterior work is not where they are currently rehabbing the interior. Sounds like the exterior work was completed already in the standard-view area and is now taking place near the pools, whereas some of the standard-view units have already been rehabbed and the preferred-view units are yet to be done. Do you have a standard or preferred view unit?
We'll be there in 3 weeks and are anxious to see the rehab progress ourselves!