I've never been to a university, so I'm merely speculating about what goes on within their walls. Listening to my girlfriend describe her experience in music lessons in high school, however, it sounds like, at least at that level, they've got it all backwards.
Schools teach you to make music that's technically correct. The private sector — record labels — want you to make music that will be popular. Schools therefore have it backwards when it comes to training people to service the needs of the industry.
This is understandable. It would be very difficult to objectively quantify how catchy a piece of music is. You could get a bunch of volunteers to — in isolation, mind — hum the piece afterwards and you could tally up how many notes they got roughly right, but such a scientific approach would be a waste of everyone's time. So schools focus instead of teaching students how to make music that's at least technically correct, even if it is boring.
Now listen to a few different pieces of music by Richard D. James, AKA Aphex Twin. Some may be great, and some may be dire. I'll wager that none of them are boring, however. When he makes a bad piece of music, it's really bad, and when he makes a good piece of music, it's really good, for one simple reason: he's not afraid to fail. He experiments. Sometimes those experiments come back negative, so to speak, but it's better to try out new things and get some hits and some misses than to be afraid to try anything at all and make bland music the rest of your life.
In high school at least — and I'd be interested to hear from someone who studied music at univeristy to learn if it's the same there or not — you're taught to pick some chords that follow on from one another well, and then to compose a melody that's technically correct when pitted against the backdrop of those chords. That's terrible advice.
As Jason Blume points out in his illuminating book Six Steps to Songwriting Success, the melody's everything, so it should be your starting point. It's what people hum in the shower. No one hums chords. If your melody's good, you can work out the backing later. If it's bad, you have to change it. No one will choose to sit down and listen to a bland melody, and they sure as hell won't pay for it. I'm paraphrasing here, of course.
James takes the opposite approach to the music students who have been scared into the straitjackets of chords. If he knows formal music theory, he seldom shows it. Perhaps he's spent decades honing his skills with trial and error, or perhaps he's spent that time learning formal theory. His fans haven't reached a consensus, which is unsurprising given his reluctance to give interviews.
Either way, what's important is that if he knows formal music theory, he only lets it guide him, he doesn't see it as a rigid set of immutable rules. He doesn't care whether his music is technically correct or not. He only cares about whether it sounds good. As many professional musicians have repeatedly said, in music, whether something sounds good or not is all that matters.
Listening to tracks like Backdoor.Berbew.Q, I'm not even sure if James knows the theory behind which notes go well together to form acceptable chords. But why should he? Even if he hasn't learnt music theory, his mind, like everyone else's, has still been shaped by listening to music his whole life. He has pretty much the same sensibilities when it comes to which notes sound good together and which don't, and if he chooses to play something that sounds hideously out of tune, it's probably on purpose.
On the other hand, if he has learnt music theory, then it's probably helped him out, but only because he doesn't let the knowledge of what works well paralyse him with fear. If that's the case, then when he chooses to play something out of tune, it's definitely on purpose.
So the real difference between James and music students is that when making music, and working out which elements to keep and which to throw away, he seems to judge something's worth by how good it sounds, whereas they tend to judge it based on if it's "right" or not, something the listening and paying public doesn't care one iota about. If he wants something to sound scary, he's not afraid to break the rules in order to achieve that effect. If he wants something to sound pleasant, it may take him a little longer to work out how to do that, but he certainly gets there. And his music is never, ever bland. Sometimes painful, but never bland.
So why are music students jealous of Aphex Twin? Because, in the same way that Fight Club's narrator is jealous of Tyler Durden, Richard D. James is free in all the ways that music students are not. They are jealous of him for being able to create any music he likes with a total disregard as to whether or not what he's doing is technically correct.
If you've learnt music theory formally, how should you fix this? Disregard your painstakingly taught notions about using chords as starting points. Focus on the melody. By all means remember the rules, but remember you can break them too.
Whether something subjectively, to you, sounds good or not should be your sole criterion for keeping or destroying it. Save yourself from a career making substandard, but technically correct, background music for travel shows and toilet roll adverts. And please, let me know how you get on, so I can shut up if I'm wrong and it backfires.
Have the courage to break the rules; acquire notoreity.