Slitherine

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Starting off with an easy one: I'm aware fleet modules don't stack with each other, but do they stack with standard targeting/countermeasures modules in the other ships? e.g. if I have a 30% targeting bonus on my cruisers, and I have a carrier or capital ship with a 5% fleet targeting module, is my effective modifier 35% for the cruisers? I assume they do, simply because you're saving virtually nothing on the power/size/upkeep by removing those modules from the various ships and replacing them with only the fleet bonus, but it wouldn't be the first time I've seen something silly in a game.

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So, other than not being able to be all buddy-buddy with other races, what's the incentive to NOT glass every planet you come to that you don't intend to take? Or, for that matter, to kind of glass them to reduce the ground forces you need to take the ones you do? You can always terraform them later to remove the damage if you don't go HAM on the planet, and if you don't care about the race, you can always turn it into a sweet penal colony a la Dune's Salusa Secundus.

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ORIGINAL: Aeson

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So, other than not being able to be all buddy-buddy with other races, what's the incentive to NOT glass every planet you come to that you don't intend to take? Or, for that matter, to kind of glass them to reduce the ground forces you need to take the ones you do? You can always terraform them later to remove the damage if you don't go HAM on the planet, and if you don't care about the race, you can always turn it into a sweet penal colony a la Dune's Salusa Secundus.

Which is more valuable - a (more or less) fully-populated high-quality high-development colony, or a lifeless radioactive marble floating in space?

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If you don't care about your empire's reputation, the incentive to take a planet by conventional invasion rather than by orbital bombardent and recolonization is that you get a mostly-undamaged productive colony more or less instantly through conventional invasion. Yes, colonies will recover from orbital bombardment over time - especially if you go for a more limited bombardment rather than wiping the colony out completely - but while the colony is recovering, it isn't as valuable as it could be. Of course, if you're going to exterminate the population anyways, whether because you're playing a genocidally-xenophobic empire or because you don't want to deal with some hippie space elves whining about how they don't like being part of your empire and are really upset about how you're conquering their as-yet-independent brethren and exterminating the space teddy bears, that's perhaps less of a concern.

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Also, poor reputation hampers diplomatic relations with other empires - not just with the Ancient Guardians. Everyone else is less likely to trade with you and more likely to impose sanctions, engage in covert operations, declare war, or even wage undeclared war on you when your empire's reputation is bad than when its reputation is good. Of course, if your empire is sufficiently powerful or sufficiently far away from everyone else, that might not matter.

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I will add that in the unmodded game (though possibly not RetreatUE; I don't know what was changed in that mod off the top of my head) bombardment weapons other than the Boskarans' Shaktur FireStorm torpedoes kind of suck. Bombardment missiles are okay at bombing planets, but are specialized for it to the point that they're literally useless against ships and orbital installations, and Heavy and Massive Rail Guns, while not completely useless, are much worse than the missiles are at bombarding planets and are probably the worst ship-to-ship weapons in the game for where they are in the tech tree. One "incentive" not to bombard planets would therefore be that if you aren't going to bombard planets then you don't need to bother developing specialized bombardment weapons and maintaining specialized bombardment ships.

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ORIGINAL: Retreat1970

In RetreatUE all races research planetary shielding around mid to mid late game. They also research planetary fortress (?) at mid game. Eventually bombardment wont work and invasions will be costly (+100% def). It varies race to race but construction of the previous two facilities can commence at 500M to 1000M colony pop.