We have been to Aquatica, Typhoon and Blizzard Beach, and would rank them in that order.
Aquatica gets the overall nod for their awesome tubeless rapids (soooo much fun) and the fact that you can rent a cabana for a very reasonable price in comparison to the Disney waterparks (standard cabanas range from $49 to $149 per day in March, depending on when their visit falls, and include rental towels, an in-cabana large locker, a fridge stocked with 12 bottles of Dasani water, and 20% off purchases at the gift shop). Disney's fee is well over $300 regardless of the season

. Their interactive kids area is HUGE and totally blows away those at the Disney waterparks as well. We love seeing the wildlife (Commerson dolphins, turtles, birds, fish), we love the big sand beach (which spans both wave pools), and they offer a very reasonably priced all day buffet (not the most gourmet food available, but certainly wallet-frierndly). The park is bright and cheery, the music is fun, the slides are great, and its just overall a fabulous park to visit.
Aquatica often has some really, really good ticket deals in the off-season. Its worth checking there before purchasing. Disney will run you $50+ for a one-day visit, but I have seen Aquatica tix for $19.
Typhoon Lagoon is our runner up. Its lush and tropical. The wave pool is the gem of the park, and so very fun (but beware....the waves are powerful enough to toss my 300 pound, 6' 4" DH around like a guppy). You can swim with the sharks. Its very well themed, and you can often meet Lilo and Stitch. Their mini donuts are da bomb

, as are the waffle sandwiches. Parking is free where its a small charge at Aquatica.
Blizzard Beach was our least favourite. The snow theme definitely was not for us (but we are from the north....and snow is not what we're after when we travel to Florida). Their bobbing wave pool was a disappointment, but the theming again was excellently executed (even if it made us cringe, lol).