A slot system for weapon installing and uninstalling:
This system would allow for better customization of weapons and their locations. It would use a specialized interface for installing and uninstalling weapons (and perhaps, other equipment if we can find a use for it) to allow you to keep the position of old weapons. For instance, say you want to replace that aging turbolaser on your pirate frigate, you would just remove the turbolaser from the slot, and put the new one in the same slot, which would allow it to fire from the same location.
Weapon management:
I can't be the only one who finds that the current system is lacking. Take (again

Better solar panels for later on in game:
Let's face it, later on in game, once you get the 500MW or 1000MW reactors and the equipment to go with, old solar panels just don't cut it. Perhaps there could be a better solar panel, like a solar array (a group of regular panels) that only take up one device slot, which would cost significantly more and generate enough fuel to power the high end reactors.
A use for ore:
Ore has ever had much of a use in Transcendence besides to sell, so instead, how about allowing you to use them to build things like ships and weapon? This could allow shipyards to be become more than over-glorified stations. This too would use a specialized interface where you can specify both what you want to build, and where the materials come from (like say you have no money but the materials in your hold, you can tell it to use the materials from your hold, and vice versa) and it would specify how much ore of what ore you need, and how much credits it would cost to begin the construction process. Ships will also come default with the weapons, armor, etc they have specified in their xml. This could also allow for a good mining system and a broader range of minerals. Also, if you build a ship, you could have some options for its use, you could use it as your own ship, replacing your old ship, you could use it as an escort, or you could sell it. The docking screen might have to be overhauled for this and the below option.
An alternative system to the above:
Instead of building a ship and whatnot, you could purchase one from a shipyard. Would show what equipment, an the stats this ship has in a description box or something to the likes (also a description box of the ship history or whatever could be cool too).
Paid escorts:
You would be able to purchase escorts at certain stations, and there could be a better ordering system to tell them what to do, too. A limit on the number of escorts would be good to keep the game from getting too easy.
More 'modular' ships:
Upgrades to your ship that would change its appearance noticeably. As to what these upgrades are and do, I'm not so sure at the moment.
I've got some more ideas but since it's 1:14 AM in the morning I probably should be getting some sleep. I'll post them tomorrow.