I can see pros and cons to this. The pros are obvious and are just like you state: you will be gaining specific expertise, you'll be doing truly independent research , you'll be pioneering.
I would point out one major con though: if you do work that none of your professors are "in charge" of there is a good chance they will act like little babies and discredit, ignore, or openly assault your work! It happened to me.
I had my master's thesis in Scientific Visualization, which was an already funded idea hosted by my advisor. Unfortunately it wasn't a very popular idea so a) it wasn't that interesting, and b) I couldn't get much attention from my advisor. But then my friend, who was doing research in Computational Biology came up with a really great idea for a collaborative visualization project and I started working on that in parallel. It turned out to be really cool, I got a poster accepted to a major conference, and my friend actually benefitted from the output.
My advisor, however, was just pissed off. He didn't give a shit that I was doing my own creative work. He just saw that I wasn't playing his game. I actually got in trouble for this. I tried to appeal to my team of 3 professors who were my secondary advisors but they reamed me too. One of them said "well none of us know if your work is actually quality. Anyone can get a poster published." Mind you out of the entire group of 12 students who submitted work to the conference only 3 posters were chosen and two of them were mine.
So the short of it is: academics are like little boys tied to their mother's apron strings. Don't expect them to support you in being truly creative. If you follow this path then make sure you either convince a professor that it was his