*SNIP*
You can already do all of those things that you say you want to do, and none of the things you say you are obligated to do, and still make plenty of money. I have not run drugs once in either this version or the last, simply because its boring and a player doesn't need to. Any of those things you really want to do: just go do them. Its fun.
But people will do drug running because its the "best", where "best" is the most/fastest/easiest, not interesting or fun. Since a better game is one where people spend there time doing interesting things rather than boring things:
(a) drug runs need to become more interesting or (b) drug runs need to be nerfed into the ground so that people don't do them.
Personally, I vote for option (a), and thats going to come with restrictions and gameplay challenges to overcome: more pirate patrols to sneak by. No access to the black market without contacts or sneaking. Hunter fleets coming after the player. Surprise inspections by main faction patrols once the player gets a reputation as a smuggler... etc. There are lots of ways it could be done.
^ HELL YES to the bolded portion! Glad to know that that's the primary instinct.
After I've had some time to think about it, I think the root issue here is that the game has grown a LOT in this release and some parts of the game are still catching up.
For the first time, the economy in general works at scale - so large-scale drug running is as possible and lucrative as it should be.
But also the system through which faction fleets threaten and interact with the player hasn't grown enough to match that pace.
Like how apparently none of the lawful factions care when you're regularly running 4000 units of drugs in one trade route and how it doesn't occur to anyone to try to confiscate/steal it from you. Or how getting caught with said 4000 units of drugs will be a minor relations penalty rather than getting you declared an outlaw or even fired from your job as a commissioned officer. Or how costs are such that there's no incentive to get into space battles that aren't horrendously lopsided in your favor, so you just quit + reload whenever you manage to lose a ship you can't recover + repair.
Also how commissions and warfare work in general. Right now, a commission with any faction is functionally the same (you get money and occasionally other factions go temporarily hostile) except for the specific ships and armaments available in their military markets - which matters less and less in the later game.
And - if a mission is particularly dangerous (which it should be) - then there should be some mechanic were you get resupplied with fresh faction ships if you take losses fighting faction enemies (which would be an incentive for players to actually make use of faction ships instead of always spamming their favorites).
Commissioned officers should probably have orders - auto-accepted missions with extra-long timers like "disrupt the port at Kapetyn Starworks". Maybe even standing orders - instead of the current standing orders of "blow up all faction enemies" it's "ship X supplies/month to Jangala" or "survey every planet in the X constellation" or "scan for smugglers in Corvus" or "supply deep-cover operatives in Tri-Tach colonies". Players should probably get their pick of long-term assignments categorized as warfare, logistics & special ops - and spend faction rep to request transfers or changes of assignment or leaves of absence.
Similarly, warfare is just doomstack fleets spawning and tossing themselves at colonies until either they decivilize or the heat death of the universe happens.
It'd be cool if there were purpose-built fleets beyond just patrols and armadas - like hyperspace interdiction task forces (which has minimum combat/burn speed requirements) and special ops units (which have insulated hulls and maybe phase ships) and deep-hyperspace ambushers (which have solar shielding and high-res sensors).
And of course there are crazy things like invasions and occupations and blockades - which I understand exist in mods but I definitely wouldn't want to see in a release before things WAY higher than them on the priority list are done.
