I will say I'm not 100% convinced yet that Fast Missile Racks + 4 Large Missiles is all that game-breaking considering how it seems to have been a player-only strategy and there are plenty of other player-only ways to overpower the game. Yes there were a lot of players talking about how good it is but that's common with any new shiny toy. Having said that, I haven't really tried it much myself though so maybe I'll change my mind once I get to try it.
If FMR + 4 LM is the issue, though, maybe it's just a matter of adjusting how FMR works. It seems like part of the issue is that its flux cost is way too low; 25% of base flux capacity when the ship sports a single Medium Missile or something is fine, but too low of a cost when the ship has 4 Large Missiles. So perhaps it's a matter of changing the skill so that the flux cost depends on the size of mounted weapons (for example, each Small costs 2%, each Medium costs 5%, each Large costs 10% of base capacity) or is a flat rate (for example, each Small costs 200 flux, each Medium costs 500 flux, each Large costs 1000 flux). This way it won't cripple the other ships that have FMR, but the player using Pegasus will end up with full flux real fast when using multiple charges at once.
Also, I think it's odd that the Pegasus has 0.6 shield efficiency, which is usually the province of good high-tech ships, and when it relies on missiles for a lot of its damage instead of brawling. That makes it too easy to survive; something between 0.8 and 1.0 would probably be better I think.
Along somewhat similar lines, I don't see why Invictus should have the same turn rate as the Onslaught with much better accel/decel and top speed. I think it'd be better if some or all of its max speed/accel/turn rates were decreased to make it more ponderous of a vessel, befitting its super long weapon range.
