It's less about the number of missiles, and more about the proportion of base flux to total flux. Pegasus has very high shield efficiency with a very low base flux pool. This means most of its flux ends up being from capacitors/hullmods/skills, so 25% base flux ends up being a rather small number.
Right, and hence a way to balance it would be to make it cost a non-trivial amount of flux. That way if you
really want to spam multiple FMR charges you could, but then you'll be vulnerable after that. The exact system or amount could come from playtesting. Just that it would need to scale properly to the Pegasus as well as the other ships which use the same system. Could also make it something like, 10% of base flux if frigate, 20% if destroyer, 30% if cruiser, 50% if capital or something, i.e. the amount depends on ship size. There are a lot of possibilities.
This makes it so that spamming FMR is still an option available to the player, but then it comes with the downside of making the ship vulnerable for some time afterward. So it becomes part of the decision of whether or not the player should spend flux for extra damage, on a weapon type where usually no flux is used (i.e. since missiles are usually flux-free).
Now, Conquest is a better battleship than Pegasus. Conquest in recent releases already blurred the line between battlecruiser and battleship.
Nah Conquest is most likely much easier to kill than Pegasus. Its shields are much worse, along with armor and hull befitting a battlecruiser.
Pegasus should live up to the name of battleship, not just firepower (whether missiles or big guns) but durability too.
It already does. That's the problem. Its shields can absorb more damage than every non-Automated ship except the Paragon, and it has better armor/hull than every non-Automated ship except the Onslaught, Legion, Invictus, and the Paragon (which has same armor but 1k more hull), and it has a lot of long-range offensive power to boot. It also has good mobility for a capital ship as well.
Simply cut FMR to one charge as multiple people suggested already. It's the most obvious solution to excessive burst and it would work. Why overcomplicate things?
Yup that can certainly work too. It seems like the problem is that players can spam multiple FMR charges too easily, in which case, the simple solution is to decrease FMR charges and/or increase how long it takes to recharge.