The balance issue is that 1v1 the kill ships can all kill each other, but during a 2v2 (the bulk of the match) they have to take more of a support role because if they get in the center of the brawl they can easily be focused and killed, leaving a teammate alone.
So you'd rather take Pyra/Support, or Junker/Support rather than Spire/support, or Mobula/support. I think this is the root of the "Pyra is OP" complaint.
Risk / Reward.
That's all it is about. Both the Pyramidion and the Junker are low risk / high reward ships since they can kill fast and provide solid support as well while being pretty durable.
The Mobula and the Spire can potentialy be better, but only on paper, in the real game, they just too weak and too easily disabled to have potential in a 2v2.
The Galleon's weaknesses are more than offset by its immense firepower hence why it's a brutal enemy with a good ally.
The Pyra is not OP, just overused because it's simple.
The Junker has way too many upsides with just 2 major weaknesses, its relatively 'slow' speed and weak hull, with the second one not realy mattering that much since in order to not die in one armor break you need a hull that will survive the burst of damage you will receive as long as your armor is down, only 2 ships realy can do that reliably so far and that's the Goldfish and the Galleon.
Here is a simple example (Caution, very basic.) of why focusing on disabling isn't realy as efficient as straight out kill builds:
Enemy team runs: 2 Kill
Your team runs: 1 Kill, 1 Disable
Enemy team has double the killing power. You have 1 disabling power though.
So in a normal fight if everything goes according to plan (Very rarely) you will disable on of their ships, meaning their kill power should be 1 instead of 2 for a short time. So basically you just slightly prolong the fight and rely on your ally to take them out.
Now if they take out your ally, even if you killed one of them they still have 1 killing power, you have 1 disable power, but because things aren't that simple, they can still kill you while you can't, so you will have to run away.
Not sure if my point made it across.. explaining it is hard. xC