After ~50 years have passed and my serious military fleets are rolling off the production lines with division troop transports and multiple wings of destroyers and cruisers, I like to add a heavily armored 36kton meson cruiser to my individual fleets. This lets me target and destroy ground facilities (including missile defense centers) with mostly impunity through the enemy's atmosphere.

And dropping a dozen divisions on the ground surface and watching them wage war for a few months is a whole lot of fun. I never bombard an enemy homeworld unless I'm really upset with them.

Keep in mind you should assign all your combat battalions to headquarters long before you ever plan to use them in battle. They won't accumulate training points unless they are assigned to a higher headquarters. I suggest going through and assigning them all now. Even though it's tedious, you'll have to do it eventually, and the sooner you do it the better.