Great list Granite

Here's my list, not necesarily in order as many things are linked. Also the things that Iskariot mentions are stuff I'd really love to see. Many things on your list I haven't included here, because they are pretty obvious, like 'better missions', 'better exploration'. Orrery map would also be a great feature.
I think PP linked missions is a big one, the grind really needs to go and be replaced by actual moment to moment needs of each Power as they go about their ways. I touch on that just quickly below,
'Context Aware' NPC's and greater NPC interaction
You meet them everywhere you go, so really the interactions you have with them should be drastically improved. Currently all NPC's come across as silly, unaware and very robotic. A more involved chat system for NPC's, taking into account various situational information and feeding that back into things NPC's say, could help in generating much more lively and human sounding responses. NPC's already can tell whether you're carrying nothing or something, or which Power you're working for... but the whole thing needs to go much deeper. I kind of see this as a 'low hanging fruit', since it seems like a simple job which can be expanded on indefinitely and will bring a lot to the NPC experience.
More info
here
Robust supply/demand logic
Provide defined values for things such as - how much aluminium does it take to build a Clipper (are Clippers built out of aluminium? I have no idea), or how much does a Terrain Enrichment System boost agricultural output. A robust supply/demand economy would provide ED the authenticty and coherence which is so missing currently. This system should underpin everything in the game... A Power wants to build large ships for their war effort? How much do they need in the way of a particular resource? That number should be known, and missions posted to the PP bulletin board on whatever needs to be done in order to get those resources- collect ore, metals, etc.
More dynamic markets
Ties into previous, but relating more to how markets are affected by events and politics. A couple of examples...
1. A system under new political control decides miners should be paid more for their ore, which then leads to... price of metal increasing, which then leads to... price of ships in that system increasing. Discussed by David Braben
here
2. A planet wide famine hits, cost of food skyrockets.
Planetary Flight, Landings
The explorer potential is enormous and could work simply from a space tourist/scenic flight POV. I could certainly get lost in doing that- if done right, would probably never get old. However...
Meaningful On Planet Missions
...would be better to have interesting and meaningful stuff to do down there. One potential could be in helping colonisation efforts and watching a planet's population visually growing over time. From a Powerplay perspective, the larger the population of a system the more valuable it is politically- in this way planets and colonisation can work into the larger picture of ED as a focus. This would enable Coloniser as a recognised career type, someone who nurtures planets through terraforming, boosting agriculture, taking materials back and forth from planet to station as required.
DB also spoke of 'dino hunting', which sounds cool but needs context. How about: protecting colonisers from the dangerous indigenous lifeforms? Leads to my personal no.1...
Procedural lifeforms and vegetation
Planets won't really come alive without life. Killing the same looking dinosaur thing on every planet will destroy immersion and believability quick-smart. No Mans Sky has tackled this problem and it looks like a blast. I'd love to see ED do better.
My number one feature would be to see a system in which smaller procedural plants and animals could be discovered and traded. These could be a special category of commodity, with a range of attributes of random strengths, for eg. nutrition/toxicity/medicinal potential/abundance, making them more or less attractive as market items. Species with high medicinal value could draw attention from corporations or scientists, which could then lead to missions to protect or exploit the resource. Provides new career type: Exobiologist.
Imagine taking a stroll down to your cargo room and seeing little animals there, which no-one has ever seen before.
Discussed
here