More control over the environment (galaxies, shops, general spawning, etc) would be awesome, hope that comes in soon.
As much as I would love a hyperspace/fast travel method the biggest obstacle to that at the moment appears to be sector loading speed.
Pretty much once you reach 1/4 sector size speed you start hitting issues with loading new sectors ahead of you, which results in rebounds as the sectors load in (would be great if we could get pre-loading, tunnel loading, or null loading at high velocity).
Personally the biggest issue for me is that travel is boring, its just endless staring at a tunnel screen.
Its either charge, click, charge click, while staring blankly at the screen, or running off to make a coffee while a logic drive does its thing.
Even with a max theoretical speed drive I've got enough time to make a coffee and a sandwich while going on lecics trip.
Pretty much once you are on your way there is nothing to do, and nothing interesting can really happen (unless you somehow regularly enjoy sun diving).
There are no natural phenomena that effect a jump drive, sun diving isn't really a issue, hell worm holes are the most interesting thing I encounter.
And as everyone has already brought up, the faster we make stuff the more dispersed people get.
So my suggestion here would be a mechanic that makes it more 'interesting' the further out you go to discourage the dispersal behavior and make navigation a bit more interesting than setting a waypoint (and ultimately frustrating without infrastructure if permanently residing far out).
Increase accuracy of jump drives dependent on average local system masses, so in other words around the center of a galaxy where there are a lot of systems (mass from stars, stations, roids, etc) jump drives will have a lot of accuracy.
Out in void space between galaxys/arms or isolated systems you might as well spin the bottle and throw a piece of string in that direction.
This will also encourage further use of gates to gate over void systems as well as introduce choke point systems and the likes as you get further out.
Funny enough, this would also make high mass ships more accurate than smaller ships when jumping in low mass areas.
Add in faction point draining via stations for siege warfare and hopefully this will encourage players to be a bit more active, and give various systems actual value to fight over.
That and possibly rare resources that only spawn in some systems.