I'm not sure if I'm putting stuff in the right categories but this is what I'd like to see, I'm also grouping mid term and long term since I really have no idea what is involved in the programming process:
Fix the toolbars. I'm still having issues where I beam down to the planet and I have to drag the icons for my weapons back on to the tool bar again. This happens EVERY time. Also the icons for my bridge officers abilities constantly disappear when I'm in space. it would be nice if it remembered where I put them.
Add a sort option to the exchange. If I look up dual phaser array mk iv, i should be able to sort them according to price.
When I create a uniform for my character there should be an option to apply that "template" to all bridge officers on the ship. I hate having to go in and change their uniforms every time I get a new officer.
More ships: Nebula, Ambassador, Excelsior, Constellation, Oberth, New Orleans. Those are my top ships I'd like to see. And I personally dont care if there isnt a whole lot of customization available for them. I just want to use them! Quite honestly I'd be happy if they showed up in the C store and I could just purchase them. Also here's a thought for the Nebula. Since it has that pod that can be changed out depending on the mission, there could easily be a science/escort/cruiser version of this ship. Weapon pod, sensor pod, and there was another version with no pod, or with additional engines. Also since people tend to get bored quickly in the LT levels I would think that at LT lvl5 there should be a mid-tier ship so we can actually start customizing ourselves for science/engineer/tactical. That's where the Oberth (science), Constellation(tactical), and Excelsior (cruiser) could come into play. And again customization options on these ships can be kept at a minimum since most people just want to be able to use these ships in game.
The ability to upgrade your ship and consoles to the next tier level. If I really like my nova class science vessel I should be able to upgrade it to a tier 3 level and so on. Adds more customization options. I know lots of people that really like a certain ship and once they get to it dont want to trade out of it, but are forced to in order to get better bridge officer abilities, more weapons and so on.
A defined XO/First officer console on all ships. It would be great to be able to pick a specific Boff as my XO and have a console on the ship for them. It should be a generic console so the XO can be whatever we want, be it tactical/science/engineer. Again it adds more customization.
Multi-ship missions for single player. Hopefully I can explain this well enough. There were episodes of TNG where Data or Riker ended up temporarily in command of another ship to help out the Enterprise because thie mission needed more than 1 ship. It would be great to have a mission where we need to bo back and pull out one of our lower tier ships, assign some boffs to it so that you have 2 ships for a single mission. Send your XO back to your T2 ship with some boffs that you dont normally use on your main ship. Gives people a reason to hold on to those older ships, or even continue to upgrade them. The 2nd ship can show up as an icon on your display and you can control it similiar to how you control your bridge officers on away missions. Wouldnt it be cool to be in a mission with a t4 science vessel that is being assisted by a T2 escort or something along those lines?