Hmmm.... not exactly sure on having it self balance. You can have someone who is a high-level gunner start piloting, and not really know how to pilot very well, despite being a higher level gunner. Despite being good at gunning, they still need experience piloting, meaning that it's going to be a relatively frustrating change from their usual tasks.
On top of that, joining players. A low level player joins mid-match and has no idea on how to make the weapon work, throwing off the good synergy the pilot and the gunner that either disconnected or left.
On top of on top of that, it would be simpler to just increase the type of ammunition types in terms of unlocks, rather than weapons. It's much simpler to lock away higher tier ammunition from lower tier players. It would make it simpler for lower levels to understand how ammunition affects different guns. Weapons would fill niche roles, while weapons add very specific buffs that they need to learn over time.
That means it would be better to add more ammo types, rather than weapon types.
I can understand weapons as a status symbol, but that starts digging into gameplay, where high-level pilots who are going into public matchs would only bring along low-level weaponry, because he isn't sure who is going to be on his ship next, while a stacked ship would usually bring along the high-skill weapons, which would be extremely powerful against low-level players, who wouldn't be able to compete as effectively.
I can kind of see how you're going for a very MMO-style leveling system, but I don't think it works well with guns. There... really isn't anything LIKE guns out there, where you are extremely dependant on your teammates, and can't really do much on your own.