You're quite correct on those big three reasons for some "creative/gameplay/content" facets being a significant dev challenge.
For me, the big "problem" areas seem to have come about when that challenging game "construct" collides with things like...
Seriously limited resources
The big push in 2014 saw the game officially released as a viable product... but some areas were noticeably minimum viable product (and that's something several FD people openly commented on).
This has left a number of legacy items that will be a hard sell internally to rework; any reworking will take resources off new features that can drive sales. While it's not impossible to make a case for resourcing such things, it's going to be tough to justify from a business standpoint.
Example:
The in-space supercruise dropout transition. There simply isn't one; a pregnant pause. The nearby planet can jump from one distance to a closer distance. Space station will "zoom in" from directly ahead, even if you technically flew pastthem in the last second of SC approach.
Contrast that to the Horizons transition, which runs a beautiful "start-to-finish" animated interpolation between the "drop" trigger point and the "glide" start point. You can tell FD threw extra planning, tech and resources at it, in an effort to avoid repeating the in-space transition experience.
But how hard is it going to be to revisit the in-space transition, instead of coding up, say, a cool fighter launch sequence for up-coming Horizons point-release? Hard.
Risk Minimisation
Some ED functionality seems to have been deliberately "firewalled" from existing mechanics, presumably to avoid multiplying the damage that bugs and unforeseen game mechanic "gaps" can cause.
Example:
PowerPlay and... well... practically everything else in the game. My guess is that the BGS' complexity-induced migraine was so painful that PowerPlay was built almost entirely in isolation. That isolation could be pitched as a positive (optional content - "you don't have to play it"), but it ended up feeling like a different board game concept slapped on top of Elite. Interestingly, despite the almost total disconnect of that extra game layer, PowerPlay and the BGS have still been caught fighting each other, and have had to be separated - see the recent mini-update patch! Some things are crying out for integration, but FD will have to tread carefully to avoid breaking other stuff. Again, new features could continue to be resourced instead of risky reworks that could make things worse before they deliver net improvements. Troubling, but true, I feel.
Momentary Lack of Focus on Consistency
Some of my personal trip-ups in Elite seem to have come about via a design process that perhaps hasn't valued consistency as highly as expediency. And I'm not really talking here about Big Gameplay Vision stuff, like flight model (how FD want ship movement to be), the need to dock to check commodity prices, etc. No, there are plenty of little things that just smack me right in the chops whenever I come across them.
Example:
Outside of special salvage missions, a cargo canister found floating in space is always "illegal salvage", but a cargo canister on a planet's surface always seems to be "legal salvage". Why is it legal? How about if I find one in space, drop it on the surface, and then pick it up again? Is it legal then? Why or why not? What's the rationale here?
Little stuff like this just makes me confused about the design process that spawned it.
I'd love to see FD continue to have enough development resources to do top-class work on Elite. I do wonder, though, whether some work to date has been
(a) rather too thinly resourced to properly deliver coherent gameplay mechanics in the challenging game world
(b) suffered from slightly too much risk-averse thinking, and
(c) not had a laser-like focus on overall consistency.
If each of those three points is address for any given future feature, and that feature is designed first and foremost from a creative perspective, it could turn the ED galaxy from a set of individual whirring mechanical cogs into something that feels like a marvellous ecosystem in action.
Which would be something to behold.