We've probably left the realm of "Quality of Life" changes and wandered into "fanciful features" a long time ago.. so in that vein:
I'd love the ability to make some random encounters persistent; with 'tracker beacons'. I often get jumped by a NPC pirate who runs away and I want to hunt him down. Or I drop into a distress call but don't have fuel limpets, and if I leave to get them the signal source disappears. It'd be great if I could fire a tracker beacon at a targeted ship and it becomes trackable via the Galaxy Map. Or for signal sources, just drop a tracker beacon and that signal source becomes a bookmark, and an in-game signal source that I can leave and find again.