Neon Genesis Evangelion Ending...
Spoilers
it was created early enough that this change wouldn't have been as trope-worthy, but I would have changed it so that the invaders were created from an initial AI build by the corporation that was making the suits, one that went rogue...
This would have lead to a final enemy as opposed to the amalgam ending of a cyclical timeline of sorts.
It also could have lead to a second series where the AI created, before it was destroyed by the heroes, an entire civilization that could be fought by the heroes and go from there.
Just felt like it had sooooo much more potential and could have had solid endings while continuing a story.