Not all of us GMs are master writers, not all of us are going to come up with an exciting original plot when we need it. When we have these troubles we fall back to old favorites; to familiar story structures. There's nothing wrong with that, it's a testament to the power of the hero's journey and similar classic story structures that we keep coming back to them over and over. The details we change, but the underlying course of the story we tend to keep the same.
Recently, I took part in a discussion about finding ways out from under the shadow of cliché. The conversation didn't start that way as such, but it ended up becoming something of a brainstorming session for story ideas. In the course of discussion I applied one of my core techniques for subverting expectations:
When in doubt, flip it on its head.
The specific example evades my memory at the moment but as an example lets look at the trope of the time traveling warriors trying to alternately either kill or save some yet to be born hero (e.g. Terminator). There's two easy ways to do this, and a third that they actually did (kinda) in the most recent movie. I'll not spoil the film but still I can suggest two ways to flip that story structure around and surprise your players.
Firstly, if your PCs are the ones to be traveling back in time to "save the future" you can throw things for a loop by having them fail. Hard. And early too. This may seem a cruel and dickish thing to do, but if you establish you time travel rules early on then once they realize they haven't ceased to exist from paradox or timeline erasure they will get sucked into stopping things from getting worse. Your ultimate payoff should be that the person they went back to save (John Connor) is actually one of the PCs who survives to become the "savior of the future" or whatever. That person he sent you back to save that you failed to protect? A red herring designed to keep the evil AI from wiping him out.
Option two; if your players are people in the present and the target for the evil person, shake things up by having the warring travelers show up from somewhere not the future. The could time travel forward from the past (Morgana le Fey and Merlin popping forward to the 20th century to duke it out over a group of teenage nascent sorcerers could be really amusing), or another reality entirely (a game of The Strange where for some reason the Quiet Cabal and the Karum are fighting over the life of a person who is not even quickened yet). If you do it right this may not even end up conjuring up any thoughts about the inspiration source at all.
By simply taking one or more expected aspect of the story to come and reversing it, or changing its targeting, you can reinvent your stories in ways unexpected by your players. So embrace those tropes and well worn plot points, just flip them upside down, or backwards, or inside out so they have new and fresh feel.