I had the opportunity to go to DL in Cali a few months ago for my first time (I'm a Floridian). Here is my opinion on the differences...
DL has a whole opening sequence that is cut from the Florida version. The opening sequence is "scray", like a haunted house. While it is a nice touch, it is not necessary. In fact, it was only created as filler as the original show-building was not large enough to host the ride, they had to build a larger building. This opening sequence was createed as filler to get riders from the original building to the new, larger show building.
This opening sequence actually makes sense in telling a story that I had no idea the ride was trying to tell. "Dead mean tell no tales" is echoed thoughout this sequence. The plotline has something to do with a "cursed treasure".
Also, the very beginning of DL's version had to make the transition of being in New Orleans to the Caribbean. DL does that by showing a barefoot man, sitting by a river, playing a banjo in the dark, with the exception of fierlies. WDW starts the ride with an area already themed to the Carbbean, so at WDW this transition is not necessary.
WDW has the whole fortress thing going, that DL does not have. At DL, you enter a New Orleans style building and your already on the ride. At WDW, you walk through the fortress, complete with cannons and caverns. At DL, instead of walking through caves, you ride through caves in that beginning sequence that was cut out of the WDW version.
From the pirate ship scene on, the rides are virtual clones. I seem to recall that there was more going on in the pirate ship scene at DL's version, but I can't figure out what it is, or even if more is going on there or not. Can anyone help me?
The AA figures are more modern at DL. For example, the auctioneer seems much more life-like. The sets themselves seem to be better at WDW's version. For example, the village on fire effect seems to work better at WDW's version. Lastly, WDW's last sequence with the treasure room is unique to WDW and is missing from DL's version.
There is talk of a major rehab of WDW's "classics". Scheduled for 2005 with a $30 million budget, PotC, Haunted Mansion, and It's a Small World will get new effects, AA figures, and new scenes.