I can see a mixed solution. Server side missions as they are and then you have client side missions that are more personalised and even injected to the commander during an update and you get them depending on what they have done and achieved. Things that spring to mind could be a proper implementation of a personal narative with the tech brokers, the Thargoid/Guardian ruins missions but with a bit more depth.
All would be optional as they are now, but they could lead to things such as guardian modules and the like. Sort of like mini quests that are personal to you. Not save the princess type missions, as they wouldn't make much sense in the grand scheme of things.
I also would change the name of the missions we get now to contracts as it would make more sense.
PC still doesn't have an achievements list
Tech brokers and material traders don't advertise in local / system chat, at the stations or the nav beacons. I'd prefer to see "15% off ALL ships and modules!" instead of wedding chatter, just sayin. And why don't they have big holograms out front of the stations?
Engineer missions can be postponed, by not exploring, or handing in any bounty vouchers, or delivering booze, explosives or sl... Let's not go there. But we do have a page to track our progress with them, and it could have a second tab for other, persistent until completed career missions. Like, uncle Rammy's ruins runs! Why is that not tucked away in the interface, waiting to be stumbled upon?
A third tab could be used to enrich your navy progression and replace or augment those little bars in your reputation panel. Maybe all navy calls to active duty could be sent to you directly and you can complete as many as you want in a follow on chain to directly affect (grind) your rank. What if you could select a faction to fight for, outside a CZ to report for active duty?
Or, do something else entirely. Fetch contracts, or a CG.
There are a huge number of awesome things FDev could do to put flesh on the legs but... Does it have a skeleton capable of handling the extra functionality, or would a MkII be a more cost effective and scalable move? Perhaps the new hardware could facilitate a more seamless transfer to new code, and an opportunity to beta test?
It seems logical that dedicated hardware creates an opportunity for a more stable, equitable platform. Hopefully the mission team will be able to concentrate on creative enhancements instead of exhausting themselves swingin the ol' nerf bats.