These two resorts are quite different.
The Yacht Club (while tastefully decorated) makes you feel out of place, unless you're dressed like Thurston Howell III headed out on a 3 hour tour. Dressing like Lovey doesn't help, this is definitely Thurston's club. (though it does look nice at Christmas)
The Wilderness Lodge has a great, rustic (and somewhat majestic) camping feel. Without the camping. Very comfy feeling.
The Yacht Club has Stormalong Bay. (thanks Beach Club!) The uncontested pool champion of Disney World, with the only 5 Trident ranking. This was the first pool that Disney had to fence in, to keep out non-hotel guests. (that happened years ago) Three pools that are laid out like aquatic puzzle pieces. The family pool, with a huge slide, swim in-out whirlpool, big play area with afternoon activities. The adult-ish pool, where there are sections deeper than the average tourist. And the diaper pool. (nuff said) All with artificial sand bottom.
The Wilderness Lodge has boat (and bus) access to the Magic Kingdom. Arguably a nicer experience than a bus. Though I'm not sure it's any faster. The bus system (especially at MK) has gotten fairly efficient. Though I've never tried to get on the boat after the fireworks exit stampede, as compared to the bus.
The Yacht Club has walk-in access to the Epcot, where you can see Illuminations without rubbing tattoos with +90,000 of your closest friends.
The Wilderness Lodge has the Water Parade/pageant/barge thing. A short, but nice relaxing (quieter) option to fireworks.
The Yacht Club does have the whole Boardwalk experience, which can make for a nice stroll around the evening. Plus, you can see Coney Island Chris, one of Disney World's greatest entertainers.
Both are nice hotels. But if you want to beat the heat and swim every day, Stormalong Bay will not disappoint.