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1. "Ultimate solution" problem

MoO2 always had a problem that bombardment was a kind of ultimate solution. Mid-to-late game it was easier to blast everything to ashes,rather than bother with invasions and stuff.

Such approach almost negated thatvery aspect of invasions. You had no reason NOT to bomb as moving colonists from your overpopulated planets and then rebuilding\buying building was ofter easier than dealing with assimilation and different bonuses for different races(enslaved population could be faulty farmers\builders\scientists).

IMO each change to the original mechanics should imrove adjacent not-so-popular aspects as well. I think it will be useful to implement penalties after bombardment with rehab time for planets.

Example:

1. Bombardment is successful and all buildings with colonists are wiped out.

2. Planet is issued with malus for restoration time(to clean the ashes, debris, ruins, restore athmosphere etc.). Most useful way is to use already existing mechanics of pollution.

3. After recolonization(or occupation after some bombardment) malus could be permanent or temporary. So additional "bombardment pollution" either reduce with time or could be reduced only with special buildings(akin to "alien control centers" from MoO2) like "Athmosphere regenerator" or "clean debris" or something else, it doesn't matter.

4. This approach would make invasions much more appealing and increase the popularity of mostly ignored techs that could be added additional effects like speeding up athmosphere restoration time or malus reduction or land troops techs.

5. Result - we have an option - either take planet fast but crippled, or slowly but undamaged.

In no way Galactic Civilization approach should be repeated - it has a mechanic that planet quality will be permanently reduced after bombardment. Every malus and damage should be reverertable\removable or people would just never use it for capture as it was in GalCiv.

Such approach would increase the importance of planetary invasions, planning, strategy without unnecessary micro and macrocontrol or repeated actions. Standart scheme of "burn everything and recolonize later" would be still viable but not so profitable, plus, land battle techs become not so useless. 

2. "Universal bombardment" problem

MoO2 had this another problem with uselessness of bombs as you could bombard planets with your standart guns if capital ships were present. Bombs were useful only if you used bio-weapons to preserve infrastructure. Batteries and rocket bases could be blasted with normal weapoins even with damage reduction and planetary shield and rarely were that dangerous, especially with low-class shield.

IMO it is better to either remove the ability to bombard with norm.weapons or implement a severe penalty. It is wrong when entire class of weapins rendered almost useless. So there are some possible solutions I can think of:

1. Make a separate non-combat ship class like "troop transport" that is used after battles.

2. Add damage for non-bomb bombardment. I.e. - if a ship have bombs, then bombardment proceeds as normal. If a capital shit has no bombs then it will suffer damage for, like, closing on or something or hidden batteries(could be used as a separate defense building also). This way, it would still be possible to glass small useless planets but will be dangerous to approach 8+ or fortified ones. 

It is important not to reduce mechanic to a routine or tedious mid-late game action, where players would be forced to drag bombers everywhery or suffer fleet damage from every undeveloped 3-pop rock with 2 buildings. But there's always a way to balance things out.