When PP lose a base the only negative effect is the damage of buildings, it should be more. The base should become infested and be necessary a mission to rescue it and all soldiers that where there and have no way to escape (aircraft presence) should die.
If a Phoenix Base is lost it should have more consequences | Voters | Phoenix Point
so going back to old design 
Iām not sure if that would go through for lower difficulties
If soldiers die if you refuse to do the defense mission, makes no sense. Actually, soldiers leave the base, hide into the wood next to base and wear infiltrator suits. If there are no infiltrator suits, they go naked and use their skin painting abilitiy to paint an infiltrator suit. After the pandas have damaged the base, the all soldiers (+1 if no infiltrator suit was present) go back to base.
I like the idea of base gets infested like haven get infested, so you can clear the infest.
Hopefully something like this gets implementet. Good idea!