Lot of good thoughts in here.
Honestly, I've found Dan John's writings on strength training to be really applicable to the process of analyzing and choosing martial arts systems. The importance of understanding your goal (among other things), is really huge.
Muay Thai is a great system, but everything it teaches will get you disqualified in a Judo tournament. The reverse, for the record, is also true. Neither system will completely prepare you for an MMA match.
Self-defense is a whole different animal, and most martial arts instructors don't address it well. As others have mentioned, there are elements of psychology, verbal tactics, awareness, and understanding of the legal system that are vital to understanding self-defense, but that are not taught in many martial arts schools.
Rory Miller writes very well on some of these subjects.
Tony Blauer has some great material regarding this as well.
Regardless of your goal, coaches are more important than styles. A bad instructor can make the greatest system awful .
As an analogy, consider Jillian Michaels and her butchering of the kettlebell swing. I think everyone on these boards agrees that the KB swing is a great tool, but if a friend or relative said they were taking kettlebell lessons with Jillian Michaels, we'd probably steer them elsewhere.
Find a coach that teaches in a way that address your goals and needs, and whose personality clicks with yours. Then you can worry about what the label on the door says.