I've stayed at CBR 3 times and WL 1 time. Will stay at WL again this May. CBR is my favorite moderate resort, hands down. But WL is my favorite overall (can't say favorite Deluxe, since that's the only one I've ever stayed at!

). Here are my comparisons on everything I can think of, except the pools (I don't swim, so can't say):
Rooms
CBR: Carribbean theme, although not overly so. Fridge (no additional cost), TV, phone, 2 sinks, double beds in most rooms. If you book waterview, I think you could end up seeing a pool as your water, unless they have since changed this. Maybe someone else will know; I can't remember. No balcony, but a pathway outside your door with a railway in front of it. Some people do take lawn/beach chairs and sit outside their rooms, especially if they have a water view.
WL: Rooms are larger than CBR, but not by a humungous amount. I believe fridges have been added here. Flat screen TVs now, and fairly recently refurbed rooms (although CBR was also refurbed in 2006, I believe it was). Queen sized beds in most rooms; bunk beds are an option. Most rooms have a balcony.
Food Options
CBR: 1 restaurant, Shutters. Nothing out of the ordinary there, really. Then sort of what I'd call a food court. It's good food.
WL: 2 restaurants, both very different than your normal restaurant. Artist Point (different in terms of food, like buffalo meat) and Whispering Canyon (different in terms of atmosphere). Roaring Forks is the CS place; not very big and not many options compared to CBR's food stations, sad to say.
Transportation
CBR: There is bus transportation from every "island" to various WDW location.
WL: Boat transportation from WL to Magic Kingdom; also a boat to the Contemporary and Fort Wilderness. Buses to everywhere else.
Activities
CBR: Admittedly I'm not familiar with any at CBR.
WL: The Lodge tour given most mornings by a CM. The Flag Family tradition (each morning, one guest family gets to raise the flags on top of WL; best to ask when you check in if you can be one during one day of your stay, but it's not always easy to get a slot). Electrical Water Parade comes by once per night usually; can see it from some rooms or from the beach. WL marina also is a plus. Campfire, sing-a-long, and Disney movies are all over at Fort Wilderness (a boat ride away).
Other info
CBR: Can be quite the hike from your room to the food area, shop, and arcade. Check-in and the front desk are in an entirely different building (the only mod that's like this).
WL: Can be a decent walk from your room to the parking lot/buses, but I'd say no more than 10 minutes, and that's if you walk fairly slowly. Or maybe I'm just a speedy walker.
In the end, I love both places for very different reasons. If you love the beachy feel, go the CBR route. If you think you'd like the wilderness theme, go the WL route. I don't think you could go wrong either way. But for me personally, if I had the money I'd stay at WL every time I go to WDW. I love it that much. Best of luck deciding! Send me a PM if you have more questions I didn't answer.