With current railguns, the class 2 have a slightly longer spin up time than class 1. Maybe if they used the same mechanic for the larger sizes to make them progressively harder to use?
Sounds good till you go through the perceived performance.
Variant 1: harder to handle, moderate increase in damage.
1A: Player uses these railguns, considers the result lacking for the extra effort.
1B: NPC uses these railguns, people don't notice a problem.
Result: People will ask for the railguns to be buffed.
Variant 2: harder to handle, significant increase in dmage.
2A: Player uses these railguns, is happy with what it does.
2B: NPC uses these railguns, people get shredded.
Result: players will start to complain about "unfair" NPCs and broken stuff again. Support will be busy restoring ships, which were destroyed by "bugged" NPCs. [Hard to ignore: NPCs actually do have better railgun control the players. The NPC can see that it's 0.02 ms before the gun would fire but is not on target, so it releases the fire button, saving heat and ammo. Even without latency (hardware, internet) i'd doubt that any player constantly could have that accurate timing. ]
We've been through that many times already on these forums on other things. Which had less impact than class 3/4 railguns would have. It's a no-win szenario for FD