The Fun way to Rework Ships
They probably already have this solution fully cooked up, so feedback is probably not wanted. That being said, removing the pilot-ship pairing is the key mechanic.
Have all (non-GL) characters available as pilots. They apply stats based on Zetas, Mods, Relics as they do now. However, you choose who pilots what ship. Give pilots affinity bonuses based on mastery (Tactics healers provide X). Give affinity bonuses for matching force alignments (You can have IG-88 pilot your Marauder, but it will be missing Y stats).
Make the current ship abilities tied to characters part of the base kits of the ships. And most importantly, add pilot slots to unpiloted vessels. Now our Hyena Bombers and Y Wings can survive.
This makes ships fun and customizable while also easing the pipeline to add more ships. You don't need a pilot anymore, just a ship kit.