I always thought it was weird that the army minigame ignored the tiles. Would have been a redeeming bit of fluff for all the mind-numbing micro they represented. Not that zone system is at all free of micro, sigh... I'm glad we can finally set job priorities... sorta (instead of a button that says priority, but really just disables job slots in a very awkward way).
Speaking of armies though, I was just thinking of a way they could be more than trivial busywork: let them bumrush defenses. Instead of stopping dead when engaged (sorry, I mean spin in a tight circle), let them keep moving. Let them even land on planets without asking the starbase for permission first. In fact, let them board starbases.
I know it's a wild change, but it would give all those completely meaningless ground combat modifiers some relevance. There are already countermeasures in place, like FTL interdiction in border systems. It would give the planetary shield a use too! (Why did they remove its physics research? Was the planetary shield OP??). Taking undamaged starbases should be a bloody affair, requiring the shuttles to first make the approach (potentially screened by warships), then fight unevenly. That combat width mechanic? Allow 6 defenders to fight 3 attackers (or 2 or 1, with the right starbase modules). Most species would still just shoot up the starbase until it "surrenders", but it'd be a situationally useful option.
You should also be able to do more things to an occupied world, if your government supports that sort of thing. Not just extermination, but the raiding "bombardment type" should unlock a much more efficient process if you actually hold the planet. Assimilation, too.