I think the OP is a cogent and well-reasoned analysis, as far as it goes. However, The one thing I would take issue with is the characterization of the "progression".
The problem isn't that the only progression is credits and this detracts from player agency, it's that there are so many ways to "progress" in ED. Dedicated PvP combat pilots "progression" is to be the biggest baddest cranky ol' whatsit in the galaxy and for that to be known, either by a rep in the community where folks get out of Dodge when they see you jump in or for it to be acknowledged by in-game mechanics. Explorers progress by getting their names on a lot of star systems with nice, interesting and high value planets in them, or by gaining community rep for consistently grabbing that perfect screenie which makes everyone go "wow" as you show 'em a place where nobody has been before. For a trader, there's a real feeling of "progression" when you can consistently ferret out routed that the 3rd party tools and in-game data can't hand to others on a plate, where your profits come from your superior skill at using the same data everyone else has got. Progression for a smuggler is becoming more and more the guy who can honestly say "I can get anything into anywhere, no matter what the law says or who might be in the way". Etc etc etc.
Players who value "progression" in a game have been strongly conditioned to expect this to be reflected in things like "rank", "level", "badges", or "achievements", or by becoming an ever more significant participant in an in-game story. Compared to other games ED has barely a whiff of that. You CAN find routes to that kind of "progression" in ED but they are all grindfests as if FD were waving their hands in a Jedi mind trick gesture and saying "this is not the progression you're looking for." And yet rather than valuing the progression that is engaging and rewarding in ED, folks gripe about the lack of the kind they've been conditioned to expect by other games and keep asking FD to introduce it.
Similarly, ED lacks "features" that exist in (according to folks on here anyway) "every other MMO" and yet it has other features that those "other MMOs" don't. Maybe trying to play it like "every other MMO" isn't the most rewarding approach to ED?
So to answer the OPs question of "what's plaguing Elite Dangerous", my answer would be "Players that want the game to be less 'Elite' and more 'generic MMO but with spaceships'" ED has plenty of flaws but, IM(not so)HO, going that route isn't the way to fix them. Better to keep on improving the best Elite game ever than to turn it into something else.