There are several reasons that I purchased the FZ6 (P.S. I had a 1989 BMW R100RT prior to purchasing the FZ-6). It was close, since I knew that I wanted a naked (tired of being hidden behind plastic) and 'thought' that I needed another 1000cc bike, however...
1) Styling: Plain and simple, this bike just looks cool, even when not modified. I seem to get compliments on the bike just about everywhere I go.
2) Weight: After having a 1000cc BMW with all the plastic (fairring, side luggage), I wanted something light, to allow me to have a bit more fun on the corners. This bike fit the bill perfectly.
3) Insurance: Although this was a bit of an afterthought, it is cheaper for me to insure the FZ-6 than a 1000cc machine.
4) Fuel Injection: Since I had a spending limit, I was looking for a used bike. After my BMW, I wanted a fuel injected bike, which the FZ-1 that was in my price range was not.
After adding a topcase to my bike and strapping on a waterproof bag with all the clothes, etc. needed for a 5 day trip, I took my FZ-6 around Lake Superior earlier this summer (1850 miles in 4.5 days). I was riding with 2 BMWs (2001 BMW R1000RT and 2007 K1200GS Adventure Series) and had no problems keeping pace with them. In fact, even when loaded down, when I needed a handful of throttle, the FZ-6 was more than happy to oblige.
My final view on this bike is that it's more than capable of handling virtually anything I can throw at it. I can't really think of a reason that I would recommend spending the extra money for the FZ-1. I think it's more that people 'think' they need a 1000cc bike to get the power they need.