Well, I certainly enjoyed it, and if you ever decide to give it an editing pass/minor rewrite to address the weaknesses you identified, like not foreshadowing Hikari before the reveal, or if you gain more confidence in writing Combine characters, not featuring her more after the reveal, I would definitely be interested in reading the edited version!
Personally, I like that Hanse was taken captive, because I like what you did with it once the Combine revealed it, as much as I would have perhaps preferred to see more done with it, but I completely understand the writing fatigue and desire to just get it done that lead to rising through the ending portion.
If you do end up doing a rewrite, I'd actually be really interested to see the suggestion someone made, of having the reason Hikari aided the Combine not being because the person from our reality was a Kurita stan, but rather because the 31st century personality ended up being dominant, even if she thinks otherwise, with perhaps some disparaging remarks in Hikari's internal narrative about how 'weak' she was before being inserted, done in a way that shows that the insert ended up being little more than memories to mine for advantage and perhaps a few lingering, easily-ignored moral hangups about little things like 'warcrimes', or 'empowering a brutal authoritarian regime that believes their destiny is to rule over all mankind', trivialities like that. Could even mention that she occasionally thinks she hears faint screaming in her 'old voice' when alone, or something. Of course, that's just my preference because I like fucked-up mental/existential shit like that, not anything I'm trying to force you to do if you don't want to.
Looking forward to the epilogues, and if at some point down the line you decide to revisit this story and touch it up, know that I will be ready and waiting to read it again!