From the options I can say that Matrix "Revolutions" was by far the worse of the two movies mentioned, in that I agree. The whole religion / science fiction storytelling thing has been done before many times, my personal favorite example of it would be Roger Zelazny's "Lord Of Light", The Matrix failed in what it set out to do because it failed to bring an appropriate resolution to the science fiction story and the religious meta-arc that made sense in both contexts and wrapped everything up. In many respects it failed for the same reason that "Evangelion" (for Anime fans) did, you can't gloss over the details of the ending and ignore half of the storytelling and establishment have gone on before and wind up using one aspect of the story to justify ignoring the rest of it.
That said the idea of computers taking people over is an old one, it was old even when "Ghost In The Shell" was using brain hacking. Tend to think of it in the scope of cyberpunk fiction where you have people entering virtual reality with their brains and interacting with computers that way, and all of the hacking and such that takes place there. This usually goes along with hackers downloading information into their brains via the interface and things like that. Inevitably in such stories you run into the idea of the virtual reality spawning actual intelligences, AIs, which then raises the question if people can enter virtual reality, and put part of it into their minds as data, what happens when something isn't just data enters their brain and controls them the way they control programs? It's a whole genere of science fiction, which "The Matrix" was drawing on heavily. Smith entering the real world wasn't really a problem, indeed the computer program entering reality was kind of an old idea before they did it, an dit would have been disappointing if they didn't pay homage to the trope.
By the same token the issue mentioned with "Pirates Of the Carribean" with the world actually ending has to be understood in the context of the movie. The world doesn't actually have an end, that's a manifestation of a spell allowing them to enter the realm of the dead, which is why they needed to get the assistance of a voodoo goddess, and couldn't just say sail for the edge of the map on their own. It's also why they needed to use a very specific ritualistic technique and flip the ship to escape.
As far as such things got, Pirates Of The Carribean at least wrapped up all aspects of the story, maybe not as well as it could have given the high expectations, but "Revolutions" simply did not. That said they both remained true to their concepts in the clear plot points.
Now, to finish this up for people who are bothering to read this I'm going to use "Lord Of Light" as an example of "how it's done" with the whole science fiction/religious crossover.
At it's core "Lord Of Light" is about a colony ship sent from earth that lands on a planet controlled by a bunch of malevolent energy beings. The guys crewing this ship, the military, are a bunch of genetically engineered guys with superhuman powers who fight off the threats of the planet and tame it for the colonists. Most notably a guy with massive scale energy control powers literally taking the entire energy species and imprisoning them. When the crew starts cloning the humans they are supposed to seed, they decide they want to do better than what happened on earth so instead of providing them with all of the technology they were supposed to have, they decide to have them build civilization from the beginning, while the superhumans watch over them and guide them in the guise of deities from Hindu mythology. They do things like put the entire planet under surveillance and use the cloning technology to create "reincarnation booths" where when people are going to die they enter the booth and their mind is transferred to a new body (which might not be human) based on how good the "gods" think they were on surveillance.
The predictable thing is that the story picks up after this has been going on for a few thousand years or so and a lot of the gods have gotten off on being gods and have no real plans to see people progress, and just want to run things for their own amusement. This leads to a rift in the crew, some assasinations, and a certain member of the pantheon disappearing, delcaring himself (believe it or not) The Great Buddha, and working to overthrow the rule of his old ship mates.
The entire story follows direct analogies to religious stories, where they could seem that way, but the "truth" actually involves superhumans with far future weapons duking it out. In cases where a certain story involves say the death and return of a specific character (like oh say, The Buddha) Zelazny doesn't really gloss over that, but finds a way for it to work within both paradigms. At one point having our hero climacticaly executed by his ship mates by having his molecules disassembled and scattered accross the whole planet so he couldn't revive by normal means, only to be returned centuries later by equal science fiction devices in the form of another "god" who sympathized with him having spent that time finding a way to re-combine his dispersed molecules (the character doing this having been given the chops to pull it off earlier with the story, especially when he was in opposition to the hero).
The point is that the climax of "The Matrix" was never really developed that well, the ending of the story got too mystical and forgot that it's at it's heart supposed to be a work of science fiction. What's more when it's over your left wondering what, if anything, was actually resolved. It fails in it's own analogy because as far as I can tell Neo, as the Christ figure, didn't actually bring about any kind of salvation, as much as a stay of execution.
Basically Revolutions sucked, I know exactly what they were going for, but the failed to achieve it, and as I explained above, I've seen the same basic type of story done better.