I like Atrocities idea about having troops and ship crews having crew health and being injured. That way the need for a medical ship wouldn't just be when a plague or two happens to break out somewhere.
As for making unit groupings for troops, this is my idea that I got from another game:
For infantry: Unit Component Units Total Strength
Squad - 7 troops
Platoon 4 Squads 28 "
Company 3 Platoons 84 "
Battalion 4 Companies 336 "
Regiment 4 Battalions 1344 "
if you want to go further than,
Brigade 3 Regiments
Divisoin 2 Brigades
For armour: Lance - 4 tanks
Company 3 Lances 12 "
Battalion 3 Companies 36 "
Regiment 3 Battalions 108 "
Also, I think that fighters should be allowed in ground combat. So if there are any fighters on the ground for the defending side or any fighters 1 grid around the planet for the attacking side, those should be allowed in on ground combat.