This game would be a terrific game to mod if it were modable. If you ever get around to making a remake, large update, or sequal, here might be some things to keep in mind for modability:
Custom responces when encountering ships.
Custom missions from planets.
Custom combat encounters (which can be linked to responces and missions).
There should also be flags and special encounters on planets. For example, when you visit planet A, you get a custom mission that sets flag A to 1. When you go to planet B, if flag A is 1, planet B will run a special encounter. That way we could create custom plotlines.
Custom ships, of course, would be really nice, but I suppose that's out of the question. It would have been nice if players could create their own ships which could be randomly encountered like all the others... Still, a little bit more variety would be nice next time. And how about being able to fit your ships with different weapons? I was disappointed that the original didn't have that.
Of course, when I suggest moding, I usually mean adding on to instead of replacing... Anyone ever played The Sims? Its more fun to download tons of new furniture, clothing, wallpaper, etc... than it is to replace the preexisting stuff.