I posted somewhere in this thread already, but I don't remember what I wrote and I don't remember when it was. Suffice to say...
On carriers, they're a staple of any worthwhile battlegroup in modern naval warfare (which includes space combat), and not including them is kind of wrong, really. That said, because of the lack of tactical combat, a whole extra set of techs (which would be weapon or logistic techs anyway), just to give the illusion of carriers would be kind of a waste for them to do unless carriers provided some kind of other advantage in combat...which is hard to imagine in such an abstracted combat system. If it were possible, make a module that does beam and missile or gun and missile damage and call it a fighter bay. Ah well.
In the case of planetary bombardment...I just don't get it. You invade a planet, you have different choices of how to do so, one of which involves dropping asteroids on said planet. What's the problem?
Now that said, I do think the different invasion options should each be tied to a very large, expensive module that you still have to pay (a much higher BC cost) to use. All except for traditional warfare. A corollary to this is that invading a planet should mess with your own approval and influence based on ethics. Evil gets a small approval boost and an influence penalty, neutral gets no approval bonus and a small influence penalty, and good gets a small approval penalty and no change in influence. This is because evil societies will enjoy conquest (approval bonus), but will be the most hated for it by other nations (influence penalty), while neutral civs won't care who they do and don't conquer (no effect on approval) and other civs will only be disappointed in them (small influence penalty), and yet good civs will be upset by their own conquests (approval penalty) even though most other civs will respect the needs of the greater good (no influence penalty), and thus it all balances out. These bonuses and penalties should either be monstrously big relatively speaking, or cumulative.
My only real beef with the game is that combat is so abstracted in the first place. I don't like that, I like options. I like chances to hit that can be affected by upgrades, I like weapons that ignore defense and defenses that negate such penetration. I like the arms race and the strategy of designing task-oriented ships and fleets. I like it especially when I'm going to be completely removed from combat like in GC2. If I can't command them, at least make enough options that I can do all kinds of odd things with strategy.
As others have stated, I also like the end-game genocide runs ... but I do think they should carry a heavy price, which is why I mentioned the approval and influence penalties above. Conquer too many planets or blow up too many stars in too short a number of turns, and get everyone allied against you regardless of AI traits or ethics.