Crippled by paranoia makes good dystopian planets.
I do remember someone saying cloaking was in the data files, at least partially, like they didn't finish it and were going to put in more code. And as for both cloaking AND orbital bombardment. It's not JUST the computer being able to destroy you, you can use dirty tricks on them, too. Using the logic of 'having these things is bad because the enemy gets them too' can be applied to many things.
Lets face it, if someone wants to destroy you in Gal CIV 2 in any difficulty above normal, and you aren't up to snuff, you're down. Perhaps orbital bombardment would require a ship spend a turn in orbit ahead of time, or starbases can prevent it, or something, but having stealth or bombardment isn't a bad thing, though maybe if it ever does get in people might want an option to turn it off.
I, for one, am all for more options, and more features, not less. As long as if they are majorly game altering some people can turn them off.
As for innocent looking ships being a bomb, missile, bombarder, transport, or warship in disguise, I don't see why it WOULDN'T work. Not everyone automatically can see weapons, especially if they're 'concealed' or disguised.
Maybe a dirty tactics and espionage tech tree, allowing people to make weapons and bombardment modules that can be 'concealed' for double space. Sure, a warship made to look like a cargo hauler would be not very powerful, but they would never realize it was one until it blasted their sole defender out of orbit since they figured you'd never get past their defenses.
I know I'm getting off track here, but wouldn't it be cool if there were ships patrolling and stopping ships in a time of war when they're paranoid about them carrying weapons?
As for the puppet government, funding rebellions bit, I think that'd rock. More than once (I said this on another thread) I've wanted to control a minor or planet of a major civ without taking it over. Mostly, to take advantage of their innate racial abilities, and force and/or coerce them to help me, or in exchange for protection from bigger bads.
Secondly, more than once i've played a game where a single race dominates everything, everyone hates them, and I constantly have aliens telling me we need to work together to undermine them, yet there are rarely options to do so, I think it'd be fun to fund pirates to harass them, or sabotage things, or rig elections ,etc, anything I can do to cause chaos, and even work with other lesser races to help cause the downfall of the larger, or AT LEAST suck their blood out slowly like a lamprey and profit!!!!! $$$$$
Thirdly: I'd love to just be able to do more colonialish things, fund revolutionaries, fund pirates, hire mercenary ships, privateers, raise tariffs, institute ships who stop tradeships and board them instead of just destroy them, take over planets but install puppet governments so they look to not be a part of me, etc, they'd be cool.
Well, I know most of these are impossible, and if not, very far off, but still I think it's fun to discuss. So don't anyone bother to tell me how silly or dreamish my ideas are, I know, but it's fun to consider.