So, I've been thinking about this for a while. But what about a "Mirror" option for ships. Obviously, symmetrical ships like the mobula or goldfish wouldn't gain anything from this, but the pyra, the squid, the galleon, even the spire (although I don't think much) would have a pretty different play style if the ship were "flipped". So,for example, the pyra could be in "mirror" mode and it would have its bottom deck guns on the right side. I think it could make play style a little more varied and when coop stuff comes out and there has to be "escort" missions or "defense" maps you wouldn't be limited on which side of your ship had guns.
I don't know much about balancing or programming, I'm more of a casual gamer, so I don't pretend to know the ins and outs of what it would take for something like this. But, I thought it might be a nice way to improve variety without changing (in theory) much about balancing or even take long to implement.