I played FTL enough to be able to beat it on Normal, something I never expected to be able to do (Zoltan Ship A for those curious)

The problem is, victory can be mainly achieved by a mix of cloaking (to avoid the power surges) and teleportation (to destroy the missile launchers). Anything else is is risky or just plain out not work.

Lots of cool weapons like missiles and beams are avoided because you know the last boss has strong shields and anti-missile drones. it's all about massed firepower to overcome the shields and hit the ship, and you really want maxed shields yourself which costs a lot and probably means you won't have other systems maxed (for example, drones)

Sure, you have some room to play with some particular ships. Federation Ship Super Flak Cannon will always do enough damage to take out the shields so you can use beams after that, but this strategy only works for Federation ships and even on this one, you could simply use mass lasers and have the Super Flak Cannon finish the job.

Personally, I'd love a bigger variety of bosses on FTL2 so you could try different strategies.