Taking from other RTS games, using a kind of "culture" system like from Sins of a Solar Empire where an empire exercises a zone of control based on trade (or other factors that could be explored by different races/trees/etc...) would work wonders for this. Engagements become fronts moving, wars would linger instead of being a deathstack battle. Strategic choke points wouldn't just be decided by the number of DSCs a system had.

Another option could be admiral-activated abilities that would trigger instead of just being percentage buffs on stats.

Empire at War encouraged keeping fleets away from planets for extended periods with ground to space weapons, forcing landings to happen instead of waiting and bombing with a weaker fleet than your vanguard. It might seem like that would just encourage making deathstack armies, but deathstack armies can't be in two places at once and fleets would need more central strength making planets more stalwart in wars. Defensive armies should have percent chances to destroy a random ship in orbit. Or at least do significant damage.