The more I think about it, the more I agree that ground combat should be almost entirely removed. Stellaris is a strategy game. To make planetary combat interesting, it needs to involve choices at a tactical level, which would turn the game in to Stellaris: Total War. I love sci fi ground wars and I would love a Total War game in space, but Stellaris does not have room for those extra mechanics. If Stellaris is to have tactical gameplay decisions, they have to occur in space. Planetary tactical decisions simply become an distracting extraneous layer of tedium when all the other visually and mechanically interesting stuff happens in space.
I think the best compromise is to import EU4's siege mechanics into Stellaris.
In EU4 you need a minimum number infantry to besiege a fort. For Stellaris replace infantry with spaceship-borne marines. From a lore perspective, pretend that the besieging marines are launching constant raids on the planet's surface, like the Mobile Infantry raids against the Skinnies in the Starship Troopers book.
Marines fill a slot in the ship designer. Corvette and Destroyer Marines are good at capturing/impairing/damaging enemy ships in boarding actions during space combat. Cruiser and Battleship marines are good at besieging planets and assaulting planets whose defenses have been breached. Filling more slots with marines makes a ship more resistant to boarding actions. If your empire's primary species and ethics are Strong and/or Militarist, you get bonuses to marine combat strength.
Special army types are special marine ship slot components, analogous to crystal armor plating or mining drone lasers. These special marine types have unique advantages and trade-offs. Xenomorph marines deal extra damage in offensive boarding actions, but do not contribute to the chance of capturing enemy ships or repelling enemy marines. Robot marines deal extra damage, but have increased maintenance cost (and might seize control of your ships during the AI crisis). Slave marines deal decreased damage, but cost less power in the ship designer. Titanic Beast armies have increased planetary siege and planetary assault stats, but are useless in boarding actions.
In EU4 you receive siege bonuses for having artillery in your besieging army. For Stellaris replace artillery with the bombardment power of the besieging fleet. Small weapons provide very little bombardment power, while Large weapons provide lots of bombardment power.
While besieging a planet a fleet costs extra maintenance, analogous to EU4 attrition. This models the cost of regularly resupplying the fleet with troops, fuel, and ammunition. Planets with modifiers like ring systems or magnetic fields inflict increased attrition on besieging fleets.
A planet's defensive stats increase with its number of tiles, number and level of buildings, number of pops (especially resilient pops), the level of its capitol building, and the presence/level of an FTL Jammer building.
Once you have fully sieged down a planet, you can land some of your ships on the planet, thereby garrisoning it with the ships' marines. Ungarrisoned worlds will be instantly liberated if an enemy fleets enters orbit. With a garrison, the liberating fleet will be forced to first siege down the planet.
In EU4 forts make a province impassable to enemy armies. FTL Jammer buildings fulfill a similar roll. Your fleets can freely enter an FTL Jammer system. However, as long as the Jammer is active, your fleet can only depart the system by returning along their original approach vector. You can disable the Jammer and press forward into enemy territory by detaching a fleet to besiege the planet. However, if you do this too many times in a row your main fleet will end up understrength deep in enemy territory relying on a string of exposed besieging fleet detachments to keep the road home open. Systems with multiple inhabited planets, each of which has a FTL Jammer, are a pain in the ass to pass through.
It is a relatively trivial matter to simply route your fleets through uninhabited and therefore un-jammed star systems. However, this will make your pathing more awkward, more predictable, and therefore more vulnerable to ambush.
Admirals cannot be placed in or removed from command of a fleet while the fleet is outside of friendly territory. A two-star admiral can ignore the effects of a level one FTL Jammer, a three-star admiral can ignore a level two Jammer, etc. A five-star admiral is therefore an invaluable and painstakingly cultivated asset, capable of freely traversing enemy territory in lightning offensives. Level one and level two jammers require a Planetary Administration building on the planet. Level three and level four jammers require a Planetary Capitol building on the planet.
The Empire-Capitol Complex building lets you upgrade a level four jammer into a Fleet Command Complex. The FCC gives significant combat bonuses to friendly fleets in the capital star system and gives a significant FTL speed bonus to friendly fleets departing the capital star system. This makes the capital star system a useful transit hub for defending the inner empire, and a place to gamble a decisive battle that may route the invading fleet.
