I was reading about Signs, and it seems like those were the two biggest plot nitpicks. The idea was that the aliens can jump up on the roof, so why can't they kick down a door?

Well... I think it's possible the aliens didn't jump on the roof. They may have landed there to begin with, then jumped down. So, they don't need incredible strength.

The boy's book also suggests the aliens will be physically weak because they will put more trust in their intellect than exercise. Of course, any UFO books written now are speculation, but as far as the movie goes, that was put in there for a reason.

The water thing is a bit weirder. And that line that bothered me the most was when the character played by Shyamalan said out of the blue, "I don't think they like water." We know he has to say that to foreshadow the ending, but at the instant he says it, to the audience, it seems his statement comes out of the blue. We (the audience) aren't given enough information about the location of the crop circles to conclude for ourselves that the aliens avoid water, and even if the crop circles weren't near lakes, rivers or oceans, you'd practically have to be an idiot savant to make that kind of connection. I mean, the most obvious connection between the crop circles is CROPS. So, rather than assume, "They must not like water!", I'd assume, "They must like corn!" Besides, if I didn't know any better (and I don't know how that character could have), no matter where the crop circles were in relation to big bodies of water, I would assume there'd be water nearby to water the crops! Most of the relevations regarding the plot seemed to arise naturally, but that one seemed really forced. I don't even think it had to be so forced - Shyamalan's character fought with the alien before then; why couldn't he have learned through that experience somehow that they don't like water? (A-ha, I hear you say. Maybe he did) (of course, a counter to that is that Gibson's character didn't know for sure about the water; if he DID know for sure, they could have gone to the lake like he suggested, and the entire climax wouldn't have taken place)

I also wished that Gibson's character would have just harvested his corn to get rid of the aliens' precious signs.

Another complaint I noticed about the movie was Shyamalan's tendency to not like to use special effects. That only bothered me once: When the alien is in the living room, and we zoom in on it - while simultaneously going out of focus! Oh, well. Shortly after that, though, there's a cool effect, when you can see the alien's skin change to match the pattern of the shirt of the boy he's holding.

I'm not too concerned about these plot holes. They could be explained (for instance, about the aliens coming here when the planet's 80% water - maybe they didn't know they were weak against water until they came here. Or maybe they were so bad off they had no choice but to try anyway). But they don't have much bearing on much of the enjoyment of the film.

Minority Report kind of had similar "plot holes" - like, it seemed like the detective from the justice department let it known to everyone that he didn't think the murder of Crowe was right. So, a) why did he just tell the director of precrime that, by themselves? b) even if everyone else didn't know all the details the detective told the director at that meeting, the other police STILL knew some things the detective told them. Why didn't they follow that up after he was killed?

How was Anderton really set up? So, you hire someone to pretend they killed the kid. They wait in a hotel. Then what? Anderton would never find him, so he couldn't premeditate the murder. Crowe would just sit around in the hotel for ever like a moron.

Now, AFTER it got started, once the prediction was made, it's all internally consistent. The initial prediction made a self-fulfilling prophesy. But how do you get it started? If the prediction is never made, the prediction never needs to be made

Actually, I heard an interesting theory about that. Maybe the Director didn't really set it all up. Maybe the pre-cogs did, and the Director thought he did. Anderton goes in the temple - maybe the pre-cogs predicted that would happen, or maybe they got the idea for the whole thing when they met him. They show him the mysterious death. That gets Anderton started on his investigation, which makes the Director nervous. The Director plans to set him up, like the pre-cogs knew he would. It wouldn't work if the Director just hired the guy (for reasons I explained) but then the pre-cogs finish the set up by making the intial premonition. Of course, the pre-cogs even have a motive: They want freedom, and they may want revenge for the murder of Agnes's mother. (Another theory about the film is that everything that happens after Anderton is HALOED is a halo fantasy; these two theories are inconsistent. Personally, I find that theory unlikely)

I don't know how convincing that is. It's kinda plausible, but the movie doesn't make the point itself. I've probably gone on long enough about these two movies to suggest that they really can make you think a lot about them, which is, of course, a good thing. I'm not sure everything has a perfect solution, though.