Then you're on a bad server/faction.
I play Pub side on Harbinger and occasionally Imp side but Pub is my main. I play each ship for their x2 bonus then focus on my Scout because I love that ship's maneuverability as well as its hit and run style of play.
I focus Gunships. They can kill me in 1 or 2 shots if I don't see them but if I'm on them they die. I keep a mental roster at the beginning of the game which enemy is playing a Gunship and even wait after the initial spawn to enter the fray to see if someone waits to switch to Gunship. Two Gunships side by side and one usually kills me while I focus the other but one of them will die.
Persistence can be the key to winning. It's not that there is an imbalance between the ships of Pub/Imp but the ability of the player, and persistence.