While recording myself playing, I realized that I was just kinda rolling through planetary defenses without very many ships at all. Bunch up, shoot down the three waves of missiles, and move in for the kill with basic lasers.

MoO1 handled this sort of thing with an infinite supply for missile shots and made direct fire weapons do half damage to planets, on account of the atmosphere. One or both of those would be good I think.

The atmosphere beams-damage-reduction thing could even give more of a role to ship-borne missiles, as they would be unaffected.

Missile shots being limited on ships makes a lot of sense because space is your main limitation. The missiles obviously cost next to nothing to produce, as they are instantly replenished for no cost between every fight. However, an entire planet should be able to stock enough to keep the pressure up on an invading force for more than three turns.

No matter how it is done, I do feel that sweeping aside planetary defenses so easily so early is a problem that needs a solution; there is nothing to really halt the blitzkrieg once you assemble a halfway decent fleet, and no reason to tech up much.

Missiles got nerfed pretty hard in the last balance pass, and I think they're currently weaker than they should be, but I agree that the missile bases should have more reloads than they currently do. Making reloads for ground bases unlimited would be realistic, but may be problematic balance wise. In earlier builds missile bases were dirt cheap and absolutely devastating, and that did not have good effects on gameplay (AI factions would lose entire fleets against planetary defenses, leaving the galaxy empty of ships). The issue will certainly be revisited.