My setting is Medium/ 5/ normal. Never played before, plus I’m normally strongly averse to giving the AI straight up cheat bonuses.
As for missile bases I’ve found that my missile cruisers do a pretty good job against them. More so because I can strike from range, so suffer less attrition before attacking. Plus it seems as if there are no planetary shields in this game (at least so far) as nobody has them. I did build some bombers early, but I found that a large enough stack of missile cruisers does plenty.