Beam Weapons (with FS2-style chargeup, and cool-down)
No more cliff-hanger endings (the storry in FL just stops...no We Won, no nothing, just "get a job!"
More types of guns, like mass-drivers, long range sniper cannons, arcing lightening-like guns.
More missile types (Cluster missiles that explode into a bunch of mini-missiles, swarm missiles that are always launched in packs, EMP missiles that temporarily disable a fighter, etc)
Mountable devices that have special abilities like teleport, tractor enemy ship, cloak, spectral-shield like effect, ramming shiled, etc.
Ability to upgrade a ship like mount better powerplant->can mount higher level guns & shields, upgraded armor->More HP's, and have them spread out through SP so that as you advance you can get the better and better versions of them, and the newly availible ships in that area cost more, but come with the best upgrades that area has to offer already installed.
More diffirent types of ships, with many paint-jobs, I want to see a freighter with a Bilbord-like advertisment on the side, or some tricked-out racing fighter with a crazy paint-job, or just a family "car" puddeling along from planet A to planet B, after all not everyone in Real Life(TM) drives a T-80 or an M1.
Have more interactive NPC that have more reactions besides, "you shot me, I shoot you!" I want to see NPCs cower in fear and drop their loot, or some try to run, while others try to cut a deal, stuff like that. I want to be able to try to bribe that cop that catches me while smuggeling (cardamine, artifacts, headz)or to talk down that junker who wants my 3 units of O2.
Have mini-quests that you can become involved with that happen spontanieusly during the "Got to A, kill B missions" like the NPC you are sent to kill tries to hires you to track down and kill the original employer and you can either take his deal, or you can take his scalp, and if you do take his deal it's a small 2-3 mission quest where you gotta track down the target.
I want to see my actions mentioned on the news every now and then, and have actual conversations with the bar NPCs not the "click and they spill the beans" as is right now.