Alright ... The choices are definitely weird (With POTC not being a trilogy and the whole "Matrix 3 as the worst" stuffs)
Let's begin with Matrix Revolutions: In my opinion it suffered from the "World at Stakes" syndrome. Matrix was much more about getting to know the Matrix, the real world and how this whole stuff works. It made pretty clear: There are no saviors, except for that mythical guy that might at some point free us -> we are screwed royally, but hey, this guy is promising! At least he might keep us alive a little longer, even if he isn't the One after all!
Then the two sequels happened. The Bane-Arc (I believe it was Bane, no? Haven't watched it in a while) was loose, ridiculous nonsense at best, in my opinion. Neo as "Justice" (blindfolded and trying to return the peace) was just as ridiculous.
Matrix 2 focused on finding out how to fix it, which was fine, but that was, in my opinion, the point at which the matrix itself lost its merit philosophically (I'm sure everyone here asked the question "What if all this stuff around me isn't real?" once in their life), as it became something supernatural with a bit of science-fuzz around it.
Matrix 3, thus, had to conclude this and put the world at stake - the machines stage war, infiltrate Zion, try to eradicate every single one who left. Neo's arc on the other hand focused on trying to get him into this "Justice" role, make him fix it, have Agent Smith "ruin" the matrix and turn this whole thing into an action-filled mess of nonsense. It wasn't a bad movie per say, it was just the worst in the trilogy as it had no connection whatsoever to the rest of it, apart from some loose strings and this huge arc that shouldn't even happen at all.
PotC3 is a different caliber. PotC never took itself too seriously - which is perfectly fine since it stars Johnny Depp ... I mean, really, how serious could a movie get in that case? - but now suddenly it went batshit crazy with Elizabeth being a captain, Will becoming Davy Jones, the whole fortress-of-doom-and-massive-defense-against-marine-onslaught arc, the end with Jones --- Know what? I really lost track during that movie. It was crazy. Nothing made sense, everything was perverted ... It was a steaming pile of crazy.
I'd go as far as to say: PotC 3 isn't as bad as Matrix 3 in relation to the series, as it never had the intention to be taken seriously and make much sense. PotC 3 however was a bad movie itself. It felt long-drawn and it jumped the movie's own shark very early.
What third movie do I personally consider the worst?
Godfather III, simply because it felt like a cheap reboot of two movies that were near-perfect together.