All you have to do is get out of arcs, plus the pyra is pretty weak, less acceleration, rotation speed, vertical acceleration/top speed than other ships. And plus it lacks disable, so take a carronade and/or an Artemis, get rid of the guns and it can't win.
Fly a catfish. (Hwatcha goldfish.)
Take meta junker (hades/art/art, gat/ mortar, carronade/banshee, gattling/banshee)
Fly a mobula and dodge them. Then use their poor turning speed and your pretty good acceleration to get away from them.
Overpower them with the firing power of a galleon.
Knock them off arcs with mines.
Take a carrot pyramidion (carronade, Artemis.)
Flamer carro pyramidion.
Out range them.
Hell, even fly out of arcs with a squid and keep in their blind spot.
Try a dual gat, heavy flak spire, with a mine, that's harder to pull off but since a pyramidion is almost all hull, they can die to this pretty good.
It's not over powered, it has its place, and it has its counters. Plus I'm seeing less Metamidions these days if I'm honest...
I will admit though the skill floor to use one is pretty low, but still it can be beaten regardless of this.
It's important to note that gat mortar wrecks pyramidions because of all the hull they have to hit, fly at your own risk.
Speaking of which, you can block shots with every ships balloon except a pyra.
Bit of a mess of a reply but hey.