In its most basic form, the ability to change a sprite's hue and saturation on-the-fly. In other words, a simple in-game skin editor.
This would allow players to give their fleet/faction's ships their own more consistent identity, distinct from the rest of the sector.
Advanced functionality could include application of decals, and the ability to change engine trail colours. In theory it could even include kitbash bits, but that's probably too ambitious.
These custom sprites would be applicable to individual ships via the refit menu, and to Custom Production/Fleet Doctrine hull blueprints, and would be accessible across saves.