There are two main reasons for the switch: 1: The GEN II FZ1 never really fit the bill for me. 2: The FZ-09 is much more "My Style" of bike.
I do not have enough riding time under my belt to give a 100% accurate comparison; But at first blush, the FZ-09 has quite a bit more usable power. For my riding style (and riding locations), I never took full advantage of the power of an inline-4. As most can probably attest, riding at 10,000-12,000 RPM is just not feasible on the street (most of the time).
The other most notable difference is the weight. The bike feels more like the WR250X than I was expecting. So light!
It's a no-brainer! 09 is nearly 100 pounds lighter than FZ1. If I wanted a bike to be all about back roads fun, 09 would be in my garage right now! It probably gets better fuel eco than FZ1 too.
I use my FZ1 like a mini version of FJR (full luggage, plenty of boring hwy miles, commuting in cold temps.. etc), so it's a keeper. It *can* still be fun on spirited rides on country roads, but I'd rather be on something lighter with shorter wheelbase for that.