My comparison is as follows (although my "final answer" is, "stay at both!," as explained below):
LOCATION: Beach Club is superior, with the ability to walk to 2 parks and proximity to the Skyliner. Wilderness Lodge has boat and bus service close to MK, but for any other park, you'll be looking at a fairly lengthy bus ride. Yes, the boats to HS/EPCOT shut down in bad weather, but you're going to be walking in the rain in that case, regardless of whether it's because you disembarked on a bus to enter the park, or took a short walk to the gate right from your room. As far as buses, they can be slow from anywhere - you just never know. Beach Club has an advantage with those as well, though, because if you're waiting to get back to your room at the end of the night and are in a hurry, you have the option of hopping not just a Beach Club bus, but a bus for any of the Crescent Lake resorts, and then walking from there. If you're headed to Wilderness Lodge, that's the bus you've got to wait for.
THEMING: It's subjective, but Wilderness Lodge is far superior in my family's estimation. Beach Club feels much stuffier and less grand in scale.
ON-SITE DINING: Wilderness Lodge has the edge, in my opinion. Although Beaches & Cream, and Cape May, used to be well-reviewed, their reputations aren't what they used to be, and Yacht/Beach Club CS is exceptionally lackluster. In contrast, Wilderness Lodge has a great CS, a gorgeous outdoor lounge, and two decent TS restaurants.
ROOMS: Wilderness Lodge standard rooms don't have a fold-down daybed; most Beach Club ones do, which could be a plus for some, and they have about 40 extra square feet of floor space overall. If you're looking at DVC studios, the refurbed VWL ones with fold-down Murphys will be superior to the Beach Club studios, which have a tiny fold-out table under the TV Murphy, and an uncomfortable sofa bed with no place to put the cushions.
POOLS: Most people would say I'm nuts, but Beach Club's Stormalong Bay is so chaotic and big that we didn't find it terribly fun or relaxing, and the four of us kept "losing" each other in the expansive space, full of view-blocking lighthouses, fences, and other large pieces of outdoor decor. We much preferred Wilderness Lodge's more open and serene feature pool, even if it lacked the bells and whistles of Stormalong Bay (just one slide, nothing exciting, plus hot tubs, whereas Stormalong Bay has multiple slides, a sand-bottom pool, lazy river, etc.). YMMV.
VERDICT: If you're staying 4 or more nights and aren't heavy packers, consider a split stay! We love to visit EPCOT and HS while we're at a Crescent Lake resort for 2-3 nights, and then switch to a monorail/MK-area resort for 2-3 nights, to focus on MK (and AK, which is 20-25 minutes from just about everywhere). Disney will transfer your luggage for you on your "switch day" while you're at the parks. By taking advantage of each hotel's proximity to certain parks, we get the best of all possible worlds.
