Wilderness Lodge is a typical Disney themed resort.......think of a nice hotel themed like a national park lodge (like Yosemite) with a themed pool, lobby etc....very nice but very hotel like, multi storied building small grounds with many rooms...........
Fort Wilderness however is a very spread out campground like resort spread over a couple hundred acres with campsites or cabins depending on your preferences.........and interspersed around the campground is local stores, restaurants, two non-themed pools, a campfire site etc.......You really feel like you are out in the woods removed from everything when you are there.....If you rent a cabin you get maid service , have your own kitched etc.......much like a dressed up mobile home......the insides are made to feel like a cabin and the outsides of the cabins are made to look like a log cabin........
As to which is better, well I've stayed at both and love them both for completely different reasons.........eally depends on what you are looking for.........both have boat transportation to MK, and bus to basically everywhere else......Everything is more convenient at WL, and more spread out at FT. Wilderness.....I like the fact that after a day of hustle and crowds at Parks you can get away and feel at peace at your cabin in the woods......other people find it isolated away from Disney feeling........also depends on what size/age your family has.......Cabins have seperate bedroom area with bunkbeds and murphy bed in living room..........Wilderness Lodge has typical hotel room interior (although you can get bunk beds).........Wilderness Lodge has a beautiful themed pool where as pools at Ft. Wilderness are nice clean standard pools....not the neat themed pools like at other resorts......
In summary its really all about what you are looking for........Hope this helps.......