Except LOTR was planned as one story from the start (not to mention the fact it was an adaptation on a book trilogy) while PotC found success in making a standalone adventure film. Everytime a series making up it's lore on the spot decides to make a two parter, it ends in disaster. The second part feels unfinished and the third part never properly finishes the story the second one began. Making parts two and three into this "epic" two part story line was really dumb and took away a lot of what made the original film great. PotC should have been the pirate equivalent of the Indiana Jones films.
Well, I understand that LOTR had great source material, and that it was planned from part 1, but the reality is that Matrix was not a horrible trilogy because it filmed the sequels back to back, it was a horrible trilogy because it was a horrible story. I'm actually a big fan of Pirates, but I know the first one is superior. Harry Potter also filmed back to back... and I'm sure those movies will be good quality film making. Filming back to back, gives you the ability to plan two movies at the same time, which I think can be a positive thing. I also know it is cheaper, it helps with continuity. So I think there is more positive aspects of it then negative. Those who failed at it, just failed a making good movies period... I don't think the fact that they filmed back to back changed the fact they couldn't even handle making one good movie.