I dont think we can really say anything about the affect of orbital bombardment on recolonization efforts because theres not enough detail. All that can be said is that if you want to have an easier time recolonizing, you have to be more careful with how and where you bomb and vice-versa. Obviously a successful invasion is going to give you the easiest recolonization efforts. I would say to reflect that you might get a bonus to population growth when you acquire the planet. Upgrades included/time invested would be a matter of balance.
If you're looking for a ship that's weak with little armaments to serve as the troop transport, then I would make it the colony frigate. That makes some sense.
The reason I was suggesting the siege frigate was that I feel that ship isnt used much and would be a primary component of an actual fleet. I would also like to avoid adding a new, underused ship. So, expanding the capabilities of the siege frigate makes sense to me and all 3 races have one. It also makes sense (to me) that it might serve as a troop transport to cover all aspects of sieging in one such specialized ship. That way, the 'siegability' of a fleet is directly proportional to the number of siege ships. It also gives you more tactical options in a fight. You might see more ships coming and decide to switch to razing the planet so that you can cause the most damage to the enemy. On the other hand, maybe you're expecting an epic battle and the opponent runs away. You can then leave your siege ships to take the planet via invasion and get the planet fully populated.
Actually, now that you mentioned culture... the time an invasion takes to take over a planet could be tied to the culture level of the planet. You could invade a planet with strongly hostile culture, but it takes a long time (not drawing parallels! nope!). however, if your culture is strong there, it would be very quick.
I would also change the way the planetary defense upgrade works:
- increases max planet hp 1500->3000. Adds small garrison of troops.
- increases max planet hp 3000->4500. More troops. Time to invade increased.
- increases max planet hp 4500->6000. Shield prevents Invasion.
Now, if you had upgrade #3 and I bombed the planet below 4500 hp, you lose upgrade #3 and are now at #2. This would make a fairly realistic siege campaign where you bomb the planet to take out the shields and then invade. If you dont have the resources to beat the garrison, you're force to bomb them all.
This whole system could be implemented without adding new ships or models. just a few icons for some new abilities, some new variables, a new indicator for how many troops are on a planet, and done deal.