I was thinking what's the true nature & purpose of the ground combat and I think I will redo the system from scratch...

Ground combat, in its core, is about slowing down the conquest (after you defeated the fleet protecting the planet you need to send ground troops and wait til they do their job). A planet should have "conquest meter", once it reaches 100% the planet ownership changes. The meter should progress based on difference betwen defending and attacking infantry. Also the fleet should probably move the meter on its own (bombardment) so eventually a fleet could take over a planet without ground troops, but it would take too long to rely on it alone (like 5% per turn).

The defensive troops (regular infantry) are divided between all your planets (based on planetary defensive priority). Similarly offensive troops (stormtroopers) should be divided equally between all planets when you have invasion in progress (so if you have 100 storm troopers and attacked 5 planets on each 20 stormtroopers would be deployed). In addition, since you can deploy stormtroopers on your own planets as an additional defence, these count too (it's a trivial number of stormtroopers / number of planets that requested their presence mechanic).

This system has nice properties, it makes the player limit the number of simultaneous conquests (or these might progress too slow) and reinforcing planets has an opportunity cost (you can't use these troops for conquest).

Now, I wonder, should I complicate it more? Like non instant deployment on a planet? Or other issues you can see here?

(I would hate to reimplement it once again :))

Your shock troops should be like the real life SAS or delta force.

You can send them into a combat zone ahead of time and they are very strong and powerful but you can only deploy a handful to a planet.

They operate by stealth and sabotage, destroying equipment and government facilities ahead of an invasion but if they are found they are good as dead.

Think like the elite troop types in command and conquer such as the cyborg commando.

They should be expensive to deploy and limited in the amount of them your empire can have regardless of the empires size.

That's how it should work IMHO.

You can send them into a combat zone ahead of time and they are very strong and powerful but you can only deploy a handful to a planet.

They operate by stealth and sabotage, destroying equipment and government facilities ahead of an invasion but if they are found they are good as dead.

And what do you mean by ahead of time? Before you take control of the planet orbit?

You plan first to take the planet by force.

Before you send the full invasion force and encircle the planet from orbit you send the shock troops months before to spy and commit espionage.

The conquering of the planet is done by your rank and file troops but the shock troops make their job easier e.g. by destroying comms facilities, orbital defences, shipyards, and military infrastructure so you suffer less casualties in the invasion.

They might also do black ops regime changes so you can take the planet with a bloodless coup, changing the local government to one sympathetic with allying with your empire...

These guys should be one in a billion hero types like Rico Rodriguez from Just Cause 2...