
Here are just some small things that caught my eye:
Docking Range and venn diagram conflicts:
It seems that the docking range is about the same for everything whether it be a wreck or a station. The acutal distance may vary but it feels like the radius of "dockability" is similar. This causes a really annoying problem when you're trying to dock into one of those big circle stations with 2 small space buoys in a vertical arrangement around it. Because of the huge docking range, it is very difficult to dock in the station from the top or bottom (or wherever the buoys are).

This also happens when a ship is wrecked near a building. Specifically at the arena when one of the ships of the initial melee blew up near the HQ. Docking at the HQ became impossible after but a few missiles were adequate to move the wreck from HQ.
Idea for possible fix:
1) A docking priority layer would be one way. Something like "docking_priority = x" such that wrecks and lootables would be 1, main stations 2, residences 3, buoys 4, ect.
This way, a main station's docking range would overlap the buoys.
Problem with this could be when certain stuff totally eclipses others.
2) Remove being able to dock on certain things. Some things like buoys are just totally pointless to dock on. Its pretty cool that you can however, and read that little piece of information on its function but its also extremely obnoxious when you spend more time trying to dock than you do rummaging through the station's commerce quarters and refitting your ship.
Destructible Wrecks:
Like the example above and to help get rid of space trash. (Dull green dots everywhere without the ability to keep track of what you've looted)
I believe there was a mod that allowed you to scuttle wrecks after boarding but I can see how this may have problems with certain storyline where wrecks must be only lootable and not wreckable.
Idea for possible fix:
1) Add new button to scuttle wrecks
2) Have wrecks automatically scuttle if there is no loot left in it (players could always use dead stations for illegal storage which is more practical anyway)
2) Regarding things that shouldn't be scuttled, perhaps add a new value to wrecks like "important = true" which if true, removes the scuttle option.
Maybe something like "station = true" for wrecks too? Derelict stations are always a cool sight

EZ reverse:
Yes I know this is like asteroids TNG but note that because it is TNG, there are some things that are different. Like trying to completely stop above a station that is packed with 8 ships already. I have to constantly tune the ship because I cannot set the thrust that one key press gives me. This makes stopping in space nearly impossible.
There are many other situations too when you want one vector towards something but want to slow it down without altering your vector but is unable to do so. (Ships in Asteroids didn't have to dodge gunboats that release tsunamis of missiles at you while firing railguns just for kicks ya know. Or wait in line to get into the most popular nightclub of Trafalgar without looking like hes on crack)
Idea for possible fix:
Perhaps an enchantment (or just give it to the player to start with) that basically allows you to reverse ship facing as in EV:N. You press the back button but instead of going forward even more, your ship automatically turns towards the direction opposite of your vector. This shouldn't be too hard to implement given that you could just get what the angle of the ship is and have it act as a "rotate" command that rotates it until the ship is 180 degrees from where it started off.
Dialogue progression keys:
(During an open dialogue interface like docking)
Its interesting how certain things are bound to certain keys like how undock is U and refuel is R (I think...) but this is a double sided thing.
Whats bad about it is that its not as efficient as just having the options laid out as 1,2,3,4,..
Since you wouldn't really want to have 2 separate options on one line for the sake of not confusing the player, there isn't too huge of a benefit having one letter bound to each option. Using 1,2,3,4 would speed things up quite a bit.
Whats good about it is that all station buttons are constant. Refuel is always one binding, refitting, bars, ect. I guess once you get used to it, it may not but as bad but its still much slower.
Idea for possible fix:
Perhaps allow both 1234 and the prebindings?
There may be more but this is all I can recall for the moment...
I assume some things can be done via mods so I'll look up the wiki later.