This is already one of the best authoring tools that have ever been provided for the fans. There are a few ways to make it better and it actually looks like you have identified them already.
Custom interior maps
better options for placing items, i.e. 3d placement or 2d with item outlines
item collisions when placing, i.e. to prevent placing a beacon inside a planet
customizable alien character
lighting controls other than sky, there are workarounds now to make a mission very dark, but it is a pain in the butt.
more ship options, i.e. the ability to customize ship exteriors and a greater number of ships available
fix ship labels, i.e. Call the Romulan Warbird a Warbird instead of Dreadnaught
ability to chat in the editor
Instead of just squads of enemies it would be good to have individual enemies we can use as combat characters.
get rid of the Deep Space Encounters in the test maps. Makes it a pain if you are testing a map in a high danger sector while flying with your foundry character which is in a scout ship and a lvl1 character with no bo's.
Since this is a way to get free content for the customers to play taking some of the load off of the developers I think that the higher rated the UGC missions are they should get prizes such as c-store credits, special ships, uniforms and etc.
I have also had issues where characters on the federation bridge are unable to move from the bridge to the ready room or the turbolift. Because of this I altered my mission so that the action does not move to the ready room and dropped a wall door in front of the turbolift door but it would be better if those worked.