OP, you make an interesting point. I would agree that Disneyland's Pirates far surpasses the MK's in terms of impressiveness and overall ride experience. I would also agree that MK's is much clearer in delivering its story. However, that's not to say that Disneyland's doesn't have a cohesive story of its own - the two versions are just structured differently.
Disneyland's version of Pirates implies a definite story of going back in time to the age of piracy. When you enter the attraction and start the ride, you're in the setting of 19th century New Orleans. From the New Orleans Square facade to the banjo-strummin', gator-swimmin', man on the back porch Blue Bayou, everything here is 100% 19th century. That all ends with the first (taller) drop, and the talking skull warning of the dangers ahead. Then you're transported to the caverns - while the time period isn't clearly established, it's still implied you're there sometime after the age of piracy, with all the skeletons suggesting that the pirates had already died, the loot already plundered. This scene may have been designed to help the mental transition between the two atmospheres of 19th century New Orleans and the age of piracy. Not until after the second drop do you reach the middle of the action. You then find yourself amongst the 18th/17th century village, with the pirates looting everyone, and the main action of the ride happening. So to sum it up, it's definitely implied you had gone back in time between the start of the ride and the end, although whether most guests pick up on this is up to debate.
WDW's storyline is, by necessity, much more compact in design, but also much clearer in its delivery. Because the ride needed to be smaller, the Imagineers wasted no time/space using the ride to suggest implicit notions of time travel. Instead, they designed it so that you enter the ride
during the age of piracy. The look of Caribbean Plaza matches exactly the design of the village the pirates are sacking, and the fortress that acts as the queue ("el Castillo del Morro") further supports this setting, working to establish this 18th/17th century mood. In fact, it may actually be implied that the fortress is the very one about to be attacked by the Wicked Wench - ever notice the pirate ship in the distance as your boat is departing from the queue? Ever wonder where it was headed?
In other words, the Imagineers wisely chose not to waste 1/3 of the MK version's length to establish the ride setting as Disneyland does. Instead, they used Caribbean Plaza and the fortress queue for that purpose, allowing guests to jump pretty much straight into the action once the ride began. This may have been a detriment to the ride experience, but at least it smoothes out the story.
