Ok, this is going to sound sort of hippie, and existential so you've been warned. If you don't want to read it, stop now.
I believe that yamahas have the best fit and finish of any motorcycle available. I think that their attention to detail is first class, and they are technically some of the best motorcycles out there. That said, I have yet to ride one that I felt had a soul. It is almost like they are too finished, and nothing about it can be truely yours. I felt that way with my first one (1984), with my second one (1990), with each one I've test ridden, each one that a friend has let me ride, and even when I test rode a FJR1300 at biketoberfest. My wife wants a fz6r and I plan on getting it for her next year. It doesn't matter that I don't think it has a soul, she loves it and that is all that counts. When I ride my hondas (I have 2 right now) they have little quirks that make them different than all of the other bikes that I've ridden including the same models. I realize that to most people these quirks are blemishes, or mechanical problems that suggest that they are inferior, but to me they are what makes them "my" bikes. My Kawasaki's over the years had them, my Suzuki's had them, and the Harley that I had definately had them (actually had too many for me).
That said, mechanically, I don't think that you can go wrong with a Yami (other than carbs, air cooled as previously mentioned), and aesthetically, they are very nice, but they just aren't my cup of tea.