Funnily enough, flare guns are very useful support guns, and I've seen them being used a lot more than before for both the damage and utility. There is one thing that holds it back a fair bit though, and it's up for discussion as it might be for balancing.
Basically, I'd want to toggle when a flare goes off. Let me explain. You're in a cloud. You fire the flaregun and it just pops in your face, exposing you and your target hopefully. Well it would be great to be able to toggle the flare gun to not burst upon hitting the cloud, but instead when it hits the enemy ship. This way, on cloudy maps, you can still use the flare gun as fire support instead of the random aspect of it touching a cloud before it reaches the enemy.
Like I said, it would open up the flare gun even more as a support gun, and there might be a balancing aspect to that, but I think it would be fairly neat to have.