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I'm usually a passholder to San Diego's and while I've never been to Florida's I've seen it on TV as well as looked at the map and read a guide book on it. Based on that, they are pretty much the same with Florida winning out with an extra roller coaster and a bigger kids play area.
I'd say they are very similar, in the respect that they have the same types of aquatic life and shows (dolphin, orca, funny otter & sea lion). However, the content of the shows tend to be different, the layout and feel of the parks are different (I personally think Orlando is more walking!), and they have different rides.
The only major differences I'd say are SWSD has more small aquariums and exhibits, and it doesn't have Kraken. Also, SWSD's JTA is more of a roller coaster than water ride or dark ride.
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