This would be a great idea, but:
1. What about the legal issues involved in redistributing it? All user-submitted content would have to meet some very strict legal rules (i.e., be licensed in a way the Starfarer crew could use it without getting sued). That's very difficult, in practice; say I'm using some code SomeGuy wrote, but he hasn't explicitly put it into Public Domain or a CC license that Starfarer can legally redistribute. I don't bother telling anybody, but when it's made an "official user level", SomeGuy complains about it, or even threatens to sue.
2. Building quality new systems is never going to be as easy as a visual editor, I suspect. It's going to involve a lot of coding. The only stuff that's easy enough to do with a visual editor is pretty trivial; put a planet here, put a station there, maybe define some patrol routes. Anything past that rapidly reaches the "pretty darn hard" category.
3. Balance, as you've indicated, is a concern, but frankly that's not too hard to handle, if user-generated levels were forced to stick to Vanilla content. But if they're using Vanilla content, they're going to get stale, fast. So we'd have random users rating things, or have Starfarer's crew picking and choosing; either way, people are going to get bent out of shape.
It's pretty hard to see how these issues would get resolved well.
Probably the best way forward in terms of fleshing out the game universe would be offer some minor bounty for complete content kits for things like complex stations with more interactivity, new art, etc.
However, a lot of that is putting the cart before the horse; before anybody can offer, say, a detailed station experience where you can get lots of semi-random adventures and FedEx quests, solve a murder whodunit and generally have an experience actually worth paying out a bounty to license... the stuff, engine-side, to be able to do things like manipulate the UI in useful ways, like constructing pages of descriptive text and dialogue trees, has to exist. Massive chicken-and-egg problem, and until this stuff exists, it's probably premature to want content built.