I'm going to interpret that question as "how much change could you make from without having to hack the source code?" because mods don't usually change the engine.
The answer there is: Not a whole lot, and one of our goals for 1.0 is to try to make it easier to do such mods. Almost everything is hard-coded in the source, except for some data describing animation indices (and of course pure media content like the music itself).
The system really, honestly believes all the way through that the screen is 320x240.
The starmap, and most ship statistics, are hardcoded into the executable. So is the conversation logic, and its interaction with game state. (The strings themselves are data and easily upgraded.)
Bottom line: Star Control 2 was not written according to the modern engine/module paradigm. It's hard to do a lot with that. It's on the list of "things that would be nice to change", but since it doesn't directly affect the end-user experience, we've lowered the priority of most of it. We've been refactoring as we go along - if we need to modify it ourselves to do the port, we'll take the time to do it right. Otherwise, we praise the Precursors and leave well enough alone.
Since the source is available, and under GPL, then one could, say, take the DrawCommandQueue and related code and make an entirely different game (though this would, naturally, have to also be released under GPL if released at all), but I somehow don't think that was the question.