Ion is not good enough because it sucks in planetary bombardment. Effect is cool though.
Ion has superior range and accuracy though, very good in taking out fighters. Too bad fighters do not have any usability later in the game, except perhaps spy hunting...
If you want weapon that is pretty much good in everything, it's either quantum or missile.
Proton seems to be weak as well... Sure it bypasses shields but accuracy and damage is otherwise weak. Does not do well in planetary assaults either.
Missiles are slow but packs quite a punch! And they excels is planetary assaults.
Quantums are very good weapons but can be dangerous because they have area effect, you can hurt or even kill your own ships in close combat.
When it comes to military bases, I believe Quantum Military bases are the best. Quantums have area effect so one shot can damage multiple enemies.
