This is first impressions but I agree with the others that the Pegasus nerf seems to be less than ideal. It's a "fast" battleship but still lacks a mobility system, so it can't kite or charge into battle, and now it lacks enough long range firepower to snipe effectively as well. Compared to the Conquest that has 2 large missiles, 2 medium missiles, and 2 large ballistics that can all be fired off at the enemy at the same time depending on fit, the damage output on the Pegasus just feels anemic even when FMR is taken into account. Most large missile systems that are both off-axis and make FMR worthwhile also have very limited ammo, which means even if the ship had enough spike damage to help destroy a capital sized enemy or two, it's going to expend most of it's ammo doing so and be left as a fat eagle for the rest of the fight.
I think distinctive slot layout is almost always going to leave a stronger impression on players than ship systems. One is visually identifiable and active at all times, and is factored heavily into player decisions on loadout by default, while the other is an extra special ability that's only going to be active and affecting ship behavior some of the time. "Four large missiles" was the defining characteristic of the Pegasus, while FMR pushed it into the territory of being too unbalanced. But take away the two front larges and you end up with a ship that can't outshoot the Onslaught or Paragon (or even the Executor when not fit by idiots), and can't outmaneuver or outshoot the Conquest, while also costing more than both the Onslaught and Conquest to deploy. Right now it's just not very good. FMR on the Pegasus is still very strong, don't get me wrong, but when the common AI counter to that ability is just to keep range and PD/tank the damage, that's not really very fun. The old build needed a balance pass, but this new version doesn't seem to be it.
Edit: If I had to choose, I'd much rather prefer a visually and design distinct 4 large missile battleship with a boring ship system such as Missile Autoforge rather than a 2 large + 2 medium missile battleship with FMR.