Wow, OP, that could of been me writing that post, I have written similar several times in the past.
I have sat and thought many times about what I think causes Elite to suffer from the 'mile wide inch deep' syndrome that people talk about.
I think one of the main perpertrators is SuperCruise, for the reasons you state.
It detaches the player from the game world, allows them to zip through systems in little or no time, with little or no danger, it literally takes away the gameplay that made Elite so special in the first place.
I would of preferred to of seen a system where you accelerate, but drop out when you enter the vicinity of another 'object', much like the mini jumps in the originsl game.
I disagree with this...Supercruise makes the size of space understandable, and manageable...it IS big. To me it is the equivalent of walking around on a map in a MMO/RPG...the only difference being that in this game you actually have to work to get some of your random interactions. Or fight to not be dragged into one.
Where the complaints of superficiality come from is that nothing the game offers FEELS connected. The story line of the game has little affect on anything. Take the Emperor and succession. There could have been a lot of different local flavor missions dealing with that- 'kill x secessionists' for example....or, a little more complicated, in-system political fighting 'this faction requires y to be in position of power when Z takes over'. The lack of this type of connectivity between the top tier NPC's, and the stories they are creating is what hurts more than anything...as this scaffolding allows players to 'plug in' and become invested.
PP attempts to do this...however, there is still no localization of storyline to invest players...so it feels shallow and detached.
Think about the problem like this...in elder scrolls...you have a dragon to kill. If it was Elite...you would be able to work to upgrade your weapons, armor, skills, etc. without EVER hearing about how your training is related to the end quest...or any other story in the game...the game would just tell you that the Wizard Guild is having a party...and nothing in the game world would be used as either exposition or driving force/through rewards.
I am not asking for an on rails MMO experience by any means. However, the necessity for story/lore to infiltrate local events provides scaffolding within the game for groups to come together and have 'reason' to do so.