I can't think of any particular reason YC is better than BC, or vice-versa. The pool is shared and other amenities (e.g., restaurants) might as well be, they're so close. I think it comes down to which theme you, personally, prefer.
PROs of both: easy walk to Epcot or even HS, boat service, can stroll over to Boardwalk if desired or go to Swan/Dolphin for dining or to mini-golf at Fantasia Gardens, attractive, sedate and relaxing theming.
CONs of both: CS offerings are dismal (with Hurricane Hanna's, the poolside CS by Stormalong Bay, being the best option), layout can be confusing if you're assigned to a far-flung room and signage isn't great (we literally got lost at least once per day at Beach Club, something that's never happened to us anywhere else).
NEUTRAL: Stormalong Bay. It seems like the majority of guests love it. We hated it and found it to be a noisy, unattractive, difficult-to-access, disorganized mess - the lighthouses and bridges and rockwork made it impossible to keep eyes on our kids, and the water slides were located across the walkway in a separate, fenced-in area. YMMV, and I realize my opinion is in the minority.