This turned out way, way longer than I expected or was planning but here’s my thoughts after a week of thinking way too much on it:
Honestly the ending isn’t bad in and of itself, and some people are grasping at some thin straws to find things wrong (like muh shallow connection). Personally, I think the parts focusing on Earth and squad 13, Nana and Hachi, etc. were pretty good and fit with the rest of the show. Even the end for Hir02 is fine from a story telling perspective. I personally don’t even believe in reincarnation but in context of the story universe its sweet to think that they are two souls who love each other so much that they will always be together in similar but different forms and combinations through the ages and get to fall in love multiple times over and over again. Plus for those who wanted 100 dino babies, maybe more they are basically the parents to the new civilization because of the fact that they taught the others how to live and also created a safe world for them to live in even if it cost their lives, just as parents would do for their children. In the end their story is picked up and carried on by the others in squad 13.
VIRM not being permanently defeated in the end doesn’t matter in the context that they are just a representation of the idea that if given the choice people will choose to live forever and be eternally “content” even if it means giving up huge chunks of their humanity. Hir02 meanwhile represent the opposing idea of accepting life as short but taking it by the horns and making the most of it while it’s here. If this were Taoism VIRM are Yin characterized as cold, slow, and passive, while Hir02 are Yang characterized as hot, fast, and active.