Definitely enjoying this game, but I do agree that the Realms RTS section needs some balancing. While the enemy defenses get stronger, our own don't, and it feels like all of the previous building we've done doesn't have any effect on our efforts.
Ways to upgrade our buildings would be great. A way to break through currently-unbreakable parts would also be great, or at least a way to purify a hex from a distance. Unfortunately, the bottlenecks and shielding does make the time-limit feel suddenly far too harsh once you hit the third level of Realms infiltrations.
I would love some way to upgrade our towers or unlock new ones. The realm mode is very much "we have Creeper World at home", and I do think it's fun, but it can be tedious. Maybe the monuments or new constellations could have something like that, since most of the monuments have been useless for me at the moment. I haven't converged since I unlocked the passive light harvesters, so bonuses to base light generation feel completely pointless unless it is to prepare me for another stage of the game where you suddenly need hundreds of trillions of regular light.