What exactly should a story mission be? In my mind a story mission is a handcrafted story, where a person or a group is hiring the commander for a intricate personal agenda that spans over several missions, like for example:
example// "Commander please find my daughter, she run away. I think she has hid on a passanger ship set to Harma. The ship has just taken off, please bring her back to me!" First possibility would be to chase the passanger cruiser and use hatchbreakers to extract the cargo, where the girl was hiding. Second possibility would be to chase the ship until Harma and find a contact there, that has seen her being captured and sold to a surface base. You then would have to rescue her by raiding a base and hacking the terminal for the prisoner cells. Once the girl is freed, she has her own agenda. Next to being chased by pirates, the girl tells you about her sotry and another adventure would open, until this is solved and the story can be concluded.//
I get that it is a problem to seed a lot of different handcrafted storylines accross the bubble, since the bubble has far over 5.000 different factions in it. Either the storys where copy/paste and that wouldn't be exactly "immersing". Or it would create to much inbalace, since systems (or factions) with story missions to them would be overrun by commanders. This could impact the BGS in unwanted ways I guess.
But there still could be story missions linked to the navy progression, since these would be personal missions not affiliated with any specific faction or location. And there could be sporadic story missions generated from your crew. Those could be procedual generated and pretty random littel storys taking part in random parts of the bubble. This wouldn't throw balance off to much I hope.