<Snipped quote by CaptainManbeard>
I don't see any causal conflicts since alternate timeline versions are not the same as direct future versions of the prime individual. The way I see it, this future version comes from a parallel reality/alternate timeline, but in its future, and goes back in time/hops from timeline to timeline in order to stop or counteract their 'prime' self and alternate selves. As opposed to coming directly back from the 'prime timeline's' future, which even if we did allow an interaction would ultimately result in either a Grandfather Paradox or a very deterministic fate. Since killing or defeating one's future self doesn't mean that you won't eventually become them, then go back to start the cycle all over again.
To give an example (albeit a poorly thought out one), see InFAMOUS. Specifically Kessler, who is simply an alternate version of Cole from the future. In particular, a future where the Beast went on a rampage and he lost everything, a series of events that sparked his desire to go back and interfere in the first place. Besides the mechanics of causality, I think time powers working as you describe is fine. Even if one time travels and makes changes, assuming no branching realities where that change succeeded are created and the timeline one is currently in is altered instead, those with Quantum Shards will remain aware and unaffected by such changes.
Since our character concepts are so similar, however, I might just go the straight villain angle and nix the prime part beyond said character wanting to gather more power to prevent their alternate selves from reforging the crystal, keep the current realities as they are, prevent the inevitability of the next loop, etc.
Oh yes, I think we actually were on the same page after all about your future self idea. I went back and re-read your original post and realized I misread a part. I thought you meant that your evil version came from the future our characters were heading towards, kind of like Alternate Barry/Savitar in the Flash show, but I see now what you meant. So yeah, we can say that there are countless alternate pasts, alternate presents, and alternate futures. Some timelines are farther along than others, and there can be many different eras covered in our adventures.
Like, there could be a timeline where it's still the 1950s but aliens invaded, or a timeline where there's a zombie apocalypse going on, or a timeline where Earth has been destroyed and the remaining humans live on other planets.
And please feel free to continue on with your idea, your evil version and my Sith Lady/Lord could probably team up for a while, though I imagine he would eventually distance himself from her when she veers even farther down the path of evil than him XD. It seems your character still has some semblance of honor and a sense of greater good, but my evil character will eventually devolve into a sadistic bitch LOL.