So, there's this mod called Battleship Brainstorm that lets you upgrade your battleships with another section like a giant Ring of Guns, or a swarm of Drones that give them more hangars, how about something like that but for Fallen Empire ships instead, to balance this you could make it part of the Lost Technologies add-on and make it require Superior Designs first, this mod would add an extra section to Fallen Empire ships (all types) for one such Upgrade, and you could have several choices depending on what you want to add, maybe you could even combine all the sections eventually.

Just an idea I had for an extension to the Lost Technologies mod.