I simply must beat a dead horse and toss my two cents in regarding the Pegasus: I personally find myself agreeing with those that insist on four missile mounts. However, I disagree with the idea of removing Fast Missile Racks. It seems to me like the ship's entire identity hinges on its overwhelming capability with missiles, so the large missile array and the ship system centered around boosting missiles are equally important to the identity of the ship. FMR isn't just a flat missile ammo buff, but is an active ability that must be built around and used with some thought, like not bringing low-ammo missiles since they'd all go way too quickly, bringing an officer with Systems Expertise, saving charges for dangerous targets, etc etc.
And beyond identity, as a player, playing with a missile boat is just a lot of fun. There is something incredibly satisfying about watching a chunk of your fleet's DP focus its firepower on a single target and watch it be reduced to ash, and capitals are supposed to be the epitome of that: concentrated force. DP focused without the herding of artificially intelligent cats
So here's what I say: change the Pegasus' other stats. Pull some different levers, unrelated to its identity. Make it squishy, slow, or otherwise anemic. Gut its non-missile weaponry. Give it no slots for PD. Make all of its large missiles face backward. Increase its DP to 60, or even make it a special one-off ship like the Zig and make it 80 (missiles are of comparable power and we lack unique ships like the Zig, after all). Really any or all of the above. If FMR and four large missiles is too much after all that, I think it would be testament to a larger issue at hand. After all, a player can pay 56 DP for four large missiles and FMR via the Venture (P), which
is slow, somewhat squishy, lacking in other stats, etc. I have heard no qualms with the latter's balancing.
All those levers aside, if a more drastic change must be made, then I could see switching the ship system. I just think most ship systems to do with missile ammo would be pretty generic (like Gryphon's missile reload) or have too small an impact to really give the ship its own flair (compared to how important, say, Targeting Feed is to Heron efficacy).