Here are my reasons for liking Disneyland's better:
1. The firefly-filled bayou setting you travel through at the beginning. It's deceptively peaceful, and it gets you in the mood for what you're about to experience. I'm also a big fan of the audio-animatronic man sitting on his porch listening to "Oh Susannah." He reminds me of my grandfather, who spent most of his time doing much the same thing...
2. The Blue Bayou Restaurant - It's on the right side as you float through the bayou, and it, too, fits in perfectly. And the food is pretty great, too (Monte Christo Sandwiches are heavenly, as are the virgin Mint Juleps).
3. The Skull and Crossbones - Disneyland still has it, fortunately. And it's the original voice of X. Atencio, the master pirate who wrote "Yo Ho." I'm not sure who did the voice for Disney World's, but I never much cared for it. I also prefer its location over the drop instead of to the left side. To me, it feels like its a part of the story when it's directly in front of you.
4. Two drops - Not that I care much about cheap thrills in attractions, but in this case, it kind of helps. The first drop tells you you're leaving the present, and deposits you in a spooky, dark cave. The second drop puts you even deeper, but now you can see around you, and while you're still in a cave, now you begin to see the fates of the pirates around you.
5. More "skeleton rooms" - The fate of a number of the greedy pirates is shown, from the ones on the beach who killed each other, to the skeleton who is eternally trying to sail the ship to shore in a storm, to the two pirates who will forever be swilling drinks in the bar, to the pirate captain who died in his opulent quarters, to the skeleton sitting atop the cursed treasure. It's more lavish and more detailed than WDW's in so many more ways.
6. The conclusion - At Disneyland, once you've seen the pirates in jail, the next scene is a room that is still burning, with beams, tables, and other items appearing to be ready to fall down upon you from above. This leads to a finale of pirates shooting it out in another burning room filled with explosives. I prefer this ending to Disney World's as the two pirates in its finale are just shooting off into space. It felt completely random to me, though the vault with gold was a nice touch.
7. The exit - At Disney World, the final scene is IMMEDIATELY followed by the get out room. Then you have to take an escalator to ground level. I dislike this for two reasons: 1) it's too abrupt and rushed an ending and 2) the escalator pretty much throws you back into the modern world. At Disneyland, immediately following the shootout, you head back "up the waterfall" and slowly are reacclimated to the real world once you reach the top.
Now, I realize the drops and climbs were originally done to avoid the railroad, but they made it all work so well that riding Disney World's version has always felt like a Reader's Digest Condensed version of the attraction. I will give it one plus, though - the queue through the fort is quite nice. Disneyland's queue isn't nearly as interesting.
As for how to make it more like Disneyland's, you're right, they would most likely have to raise the entire attraction one floor, which I know would never happen. Actually, they could get away with just the one drop, but extend the beginning and the skeleton rooms, change the ending, and add in the final climb back to the ground level. Again, it will most likely never happen, but I can dream.
Sorry to go on so long, but I wanted to give you a semi-complete answer to your question.
