Starsector 0.97a is out! (02/02/24); New blog post: Planet Search Overhaul (07/13/24)
Merlin and Gargoyle are limited to only PD weapons. If you say "just change the weapons and the ship systems so they aren't overpowered", soon enough the suggestion becomes "I want superheavy fighters", which I'm not sure if you intended.
A ship with Battle-riders would be nice though. Non-replaceable, frigate (or larger) sized combat ships carried by a tender that devotes most if it's systems to carrying the riders. If the riders are customizable even better.
Riders are replaced for free between battles, and you can have riders that would be far too powerful as a standalone ship, but can be limited by being tied to a carrier.Usually the reason for Riders to exist in a setting is because they let you build ships that perform better mass-for-mass because you can leave out all the FTL drives and long-term supplies that you'd need for a "real" ship.