My thoughts run basically parallel to Garfunkel's. I've thought about this before, and have modified my last set of suggestions.
There are three bits that I'd like to see. First, more granularity in ground combat. At the moment, taking over a planet is binary, either you have it or you don't. It might be nice if larger planets had multiple sub-sections which you could conquer one at a time. Some form of terrain system might be a good idea, too. At the simplest, divide the planet into an 'urban' and a 'rural' section. The rural section has a specific type, be it 'desert' or 'forest' or 'sea', with corresponding terrain effects. Normally, you land in the 'rural' section, and have to fight your way in. Planets with big populations (>100 million pop?) could have multiple 'urban' sections.
Second, combined arms. At the moment, all ground units have two values, attack and defense. And that's all. A heavy assault battalion is better than any other battalion, and costs the same to move. Instead, define a dozen or so different types of 'combat power', and rate each unit on them. Some suggestions:
Infantry
Mobility
Armor
Artillery
Engineering
Air
Anti-Armor
Anti-Air
Recon
Fortification (granted by being dug in, not inherent)
Naval
Command and Control
Logistics (maybe)
These interact to give bonuses or penalties in combat, depending on situation, with combined arms being required to gain victory. Some types of units would do better than others in various terrains. For instance, infantry is more important in urban terrain, unless you just want to destroy everything. (And avoiding damage to their infrastructure would be a reason for the defender to deploy forces in the Rural part of the planet.) And infantry is the only thing (except maybe engineers) which can perform boarding actions and the like. Garfunkel's 'hard' and 'soft' are a somewhat simplified version of this, but I like the overall idea.
Also, ships in orbit could be counted as part of this bonus set. Fighters and bombardment platforms give bonuses on this stuff. Another aspect might be to set ROE, where you trade off firepower for reduced damage to infrastructure.
Third, more customization of units, interacting with the combined arms stuff. Let's say we have a dozen or two different elements which are used to build units. These are generally platoons or companies, and research improves each of them separately. (Maybe there'd be level techs to unlock a tier and then individual techs below that, so you can't just blitz one line, while not making specialization unduly expensive.) So you might garrison mining outposts with a battalion made of three infantry companies and a logistics element, while the 1st Armored Brigade would have three mechanized infantry companies, six armored companies, three artillery batteries, three companies of cavalry scouts, and so on.
Obviously, you'd have various types of transport to deal with this. Maybe 'personnel', 'light' and 'heavy'. 'Heavy' covers things like naval units and titans, while 'light' is anything up to tanks.