Thanks for the feedback!
The main differences between the ships of Rebel Ops and Hel's Fighters is the handling, health pool, weapons, and equipment. The Titan, for example, is really large and bulky, while the Hunter is more agile and has access to Seeker Missiles. There's also ships like the Siren with its absurd amount of speed, and the Stinger Mk2 with its laser knife weapon. The Aerostrike has the better overall handling.
The bosses do not regenerate shields based off a timer. After bosses take a certain amount of damage, they regenerate their shield and advance to the next phase of the battle. As for how to avoid the first Hel's Fighters boss's attacks, you can either try to dodge his bullets, or use nearby terrain for cover. Each corner of the boss arena has a wall you can use for that. If I do a rebalance pass on the game, I'll give it another look.
For the Campaign, I do have pending redoing the objective markers to better guide the player. That change will take some time to develop, though. As for the backgrounds, sadly I don't currently have an easy way to replace them. If I find one that isn't too time consuming or expensive, I might be able to try a few things.