As an engie I have to say the pyra is OP because it is too easy to repair. If you compare it to any other ship, it only requires 1.2 engies (yea, 1 main engie and 1/5th of a brain of the top engie), if that, to be at 100% sprayed and full rebuild potential. It also only has 1 part that is "hard to get to" which is the back left gun, which in 99% of pyras is a flare and isn't necessary to be up in the heat of combat.
Junker requires 3 fairly coordinated people to spray, 1 hwacha will instantly disable everything, back turning engines are critical and also the furthest away to repair/rebuild, also removing your gungineer from side guns. All in all you really have to strike a balance between tank and dps. For the pyra, its front guns shooting at all times, gungineer hits balloon once while reloading, main deck is fully repairing all the time. So tanky.
Galleons are huge and sucks for the top deck - balloon, hull, main engine are all 2-3 seconds away from each other, and your main engie has to watch balloon and hull (pilot can help with balloon, but ugh), and you lose your main engie on guns once you start taking hits.
Mobulas are...well you all know how mobulas are. Requires division of labor, and even with pilot on top gun you require a lot of running around for the top deck gunner/gungineer. Also if you ever start taking hits you're basically dead anyway.
Even goldfish are harder to repair - the main engine is way back there, and a general spread of back engie and front engie still requires a 2-3 second delay between side engines and balloon (when climbing up). Only salvation is the good hull placement. Hull drops so fast hull engie will face a sophie's choice whenever the balloon goes down.
Squids too! Everyone knows the back left engine is so neglected, the ramp to the hull will glitch out if you lag even slightly, getting you stuck on the side pipes where even a split second delay means your hull is down. Front gunner has to jump down and run around to hit hull, requiring 3 seconds again.
On pyras repairing is a joke and 100% spray uptime requires no effort, allowing you to go full offense without sacrificing any tankiness.
The layout is just too good. Having a wall behind the upstairs railing so they can't jump down (have to use ladder), and blocking off the main engine from below are ways to make it a bit tougher to use than its current layout.
EDIT: actually I thought of a better solution.
Place the balloon downstairs, way in the back above the back right engine. This might seem like a boon but, if it isn't hittable from below, will require a roundabout circuit for the downstairs engie, and you will be forced to drop a gunner from the top to come down once critical components start taking damage, limiting its full offensive potential.