I agree with you. Detailed abilities and reasonable specializations just seems like the natural way to go with them. But I would like to add something to the single pilot in a single ship narrative though. I've been playing for several years now. I have every ship in the game and most every one of them upgraded. I have billions upon billions of credits. It seems natural that my narrative and others in my situation would have evolved into a more corporation like enitity. I used to work for a trucking company as a dispatcher and I see much of my former job in the game. Those truckers who stayed for a long time with us wound up purchasing their own trucks, hauling loads for us that we provided and even started their own trucking companies. The narrative just seems like it could evolve a bit.
I'd much rather the narrative be expanded and strengthened for the single pilot, than to move into areas already much better represented in games like the X-series or EVE.
I'm not against your ideas in general as I enjoy management-style gaming in other games, but it seems an ill fit for the overall aim of Elite. I'd take an NPC squadron-based approach at most, where your pilots could wing up with you, but even that opens a lot of weird wormcans in terms of the effect on the game. Part of the concern on a coding level is based on FD's execution track record with existing features such as Powerplay.
My concerns are also based ingame on what I perceive as the societal strata of Elite from a worldbuilding perspective. We have dirtsiders, whose planetary/faction currency could likely not even buy 100 Credits without selling their home and the family in it. Then there's the majority of NPC pilots, who aren't much better off than dirtsiders - no escape pods for most of them! Then us in the PF, as glorified mercenaries and political agitators, backed by a powerful shadow consortium as a whole, but with individual pilots not being major players in the direct political and financial landscape no matter how wealthy we become; we're not going to be buying a Coriolis any time soon or hanging out with Princesses and Senators. After that you move to the real monies in the galaxy, the corporations, with the most powerful having their head offices on Mars.
IDK if there's room in the game to allow an expansion out of our "caste", so to speak, without losing focus on the "ima spaceman!" aspect of the game which to me is the most critical. X and EVE don't do pilot-based gameplay even a shadow of what you can get here, so I'd rather see continued focus on that.
All that said (typed really but still), if it were going to be a thing, I'd want SpaceTruckBoss to be almost a separate game from Elite proper to do the idea any kind of gameworthy justice. There's a lot of aspects that could make a good management game if properly fleshed out, but if it's just going to be a simple "Assign Pilot X to Trade Route Y, Collect Z Credits - oops rolled a 1, Pilot X is ded" then I'd rather not have it.