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Unbreakable
As much as I like this movie, the ending could've been way better, even though this was the only surprise ending of Shyamalan's that actually worked, and of his movies this one was the most tightly written.
Actual ending:
Mr. Glass is a bad guy. Surprise!
Better ending:
No surprise at all. Just a normal ending. Which would, in fact, be a surprise ending, since everyone was expecting a surprise ending. (Did I just blow your mind? It's ok if I did.) What is a surprise ending if not the confounding of expectations?
Instead, Mister I-Named-Myself-'Night'-Because-I'm-So-Cool had to go and use the same formula he used for The Sixth Sense, and by doing so, doomed himself to being a gimmick.
The Matrix Saga
Viewing the trilogy as one story, Revolutions is the third act.
Actual ending:
Nothing is done with the numerous things set up in Reloaded. The Merovingian appears for 30 seconds, even though the Merovingians were supposed to have descended from Christ and he "used to be like Neo." The Ghost Twins don't appear at all. The wooden spoon? Pointless. The Matrix's cycle? Pointless. The Kid? Pointless.
Suddenly Smith is more powerful than Neo, despite the fact that Neo is supposed to be the supreme being in the matrix. The explanation for Reloaded's ending, where Neo has powers in the real world is utterly unsatisfying. There is no surprise or twist or anything. We get an hour of fighting in Zion.
I could go on, but I won't...it would take a while.
Better ending:
They should've used what they set up in Reloaded. Do something with the Merovingian and the Kid and the wooden spoon and the Twins and all the rest. Address the issue of a multi-level matrix (see: eXistEnZ). Give a better reason for why Neo was able to stop the sentinels. God damn it.
Signs
This is where Shyamalan gave up and started pandering after the disappointing box office receipts from Unbreakable.
Actual ending:
It is discovered that the aliens's weakness is water and that God saves the family.
Better ending:
Ignoring the fact the God's intervention makes the movie incoherent, it would have been much better if the aliens's weakness was not water, because that is stupid. They would have been sustaining damage simply from being in our atmosphere, which they didn't seem to have trouble breathing. So make the weakness something else; I suggest soda. This works better for 3 reasons: 1) there is no soda in our atmosphere, it does not fall from the sky regularly, it is not present in every living thing on the planet; 2) soda is acidic; 3) it would add a nice tweak to the line that the crop circles were a hoax to sell soda.
AI: Artificial Intelligence
Actual ending:
Spielberg tacks on a ridiculous ending involving aliens and an ice age. You know, because he's a better filmmaker than Stanley Kubrick.
Better ending:
Like Becca said, stop at the Ferris Wheel/Blue Fairy scene.
Gattaca
Actual ending:
Jerome overcomes all odds and makes it into space.
Better ending:
He has a heart attack and dies during the extreme stress of space flight. Because that's what happens when people with heart defects lie and cheat to do things they shouldn't.