I think I've only seen about half of them, but I'm guessing that every protagonist has a 2188 counterpart. Each of the protagonists is a clone of their 2188 originals, through Project Ark, and the UFO. The UFO underlies (literally) a controlled community within which the Ark colonists live, governed by Universal Control. Maybe this is to support them until the surrounding planet can be terraformed to a state that humanity can spread back out, or maybe that's just how the colony has to be set up to sustain humanity?
It's not yet clear to me why the Deimos have been turned against humanity, but it seems as though the DD426 infection put a wrench into the defenders' use of the Sentinels, causing them to lose the 2064 battle catastrophically. I'm mostly on the belief that the nanomachine injections from the Magical Gun are being used to neutralize and counteract the DD426 code, allowing the Sentinels to be used again for the final battle. But it's also confusing since I originally thought that the adult, original Izumi was the voice behind Yakushiji's Fluffy, but why would he want to re-activate the Sentinels? (Also, what's up with the fact that Fluffy's actually a phantom entity? Nanomachine tomfoolery? Is it similar to Kurabe's hallucinations of his pal Shiba?)
I'm actually still not sure if the adult Ida, Izumi, and Morimura we keep seeing are the 2188 originals, or if they're third instances of those individuals. What is Okino's angle on identifying and controlling the D-Key? I don't think I have everyone's alignments worked out either. A stray thought entered my mind: what if the Sectors are physical locations designed to be like different time periods, and time travel is just spatial travel instead? I'm sure my questions will be answered, and any misconceptions will be corrected, in due time.