How about this theory? I think it's a bit different to and might be hard to understand, based on how we perceive the story as a linear movie:
After watching the movie, I still wondered how one or more entities would be able to somehow alter time in the whole universe to create the resets. A bit like The Butterfly Effect? Nah, didn't really make any sense to me.
But then I've had the idea to understand the resets in a different way:
The Mimics aren't able to time travel or reset time in any way. However, they're able to somehow transfer knowledge/memories back in time utilizing something in their blood.
While watching the movie, we always notice Cage waking up, obviously shocked by the death he experienced just moments ago. But what if he just got that memory that very moment (or just before) similar to how dreaming works. If you've ever wondered why you always wake up after a dream, it's primarily due to you remembering only the dreams right before waking up; even if some time has passed since then.
Now combine this with a video game's "save logic" and you'll get a pretty interesting (and in my opinion conclusive) solution:
Similar to a gamer, the Mimics being able to transfer memories to "save" at a specific point in time so they're able to transfer back whatever they've learned.
By default, Alphas would obviously imprint that moment in time to pretty much always be 24 hours before, offering enough reaction time without making it overly complicated (too much to remember).
The moment Cage kills the Alpha for the "first" time, he gets in contact with the blood, sending back his memories as well (which would obviously alter his own blood in some way as well).
Cage lacks the knowledge or ability to "reprogram" the alien cells or elements within his blood, so he has no way to alter the point to which his memories are sent back.
He loses the ability due to blood loss/transfers, simply due to the fact that the ratio/amount would be lowered significantly.
The Omega obviously created its own save point, but at an earlier point (explaining the time difference for the last "jump").
Once the omega is killed, memories are sent back to that morning. This happened before, they're talking about the Omega allowing them to kill it.
So the only question this doesn't answer: Why is the Omega gone after the last "jump cut"? Did it retreat or hide, since it knew the humans now possess the knowledge of how their "mind trick" works (even if it's just speculation)?
In case anyone is interested, as far as I've heard, the whole "transfer information back in time" might indeed be possible. Utilizing quantum entanglement you're able to link two or more particles, so both share the same state. While I don't really know all the little details etc. as far as I've heard, you should in theory be able to influence one particle and the second one would mimic (pun here?) this, no matter what/where. (The Mass Effect trilogy also utilizes this and uses it for its faster-than-light communication system.)
So advance this a bit: Relativity theory states that time passes at different speeds based on the objects own speed/mass. So if you move both particles indepently at different speeds etc. time for one of them would pass faster, essentially creating a link between two points in time.
So what if the Mimics are able to utilize this in some way or another as well? This still doesn't explain how the blood/infection gets back in time, but it sounds really interesting, doesn't it?