You had confused Pegasus with the Perseus, Kosh. Perseus is a Terran interceptor which have two gun banks that can carry Kaysers, Pegasus is a stealth fighter you face in one mission in FS campaign and, unfortunately, cannot fly in standard campaign (though get you fly it's Vasudan counterpart, which has larger target profile and isn't as good). It's incompatible with Kaysers and have only one bank, but has paper thin rear profile, superior speed, maneuverability and stealth capabilities, meaning that no aspect missile can lock on you (due to the bug, heatseekers can, but they are easy to dodge) and turrets will not fire at you unless you're either very close, firing weapons, or using afterburner, or there's an AWACS nearby.
Both are fun to fly, but I prefer Pegasus due to it's better speed and ability to outmaneuver most of it's enemies. It lacks in firepower and armour though, making it a flying coffin when there's AAA and flak armed enemy capship nearby (I mean serious business capships, Cain for example, doesn't count and Pegasus can kill it relatively easly. to kill a Fenris though, you have to make good use of your stealth to get to it's blind spots, or AAA fire will shred you).
EDIT: You could fly Pegasus in main campaign mission "Endgame", but it's not recommended and unless you have very specific flight style, there are better fighters for this mission.