I''ll go against the group here and say it's probably not worth it. Unless you're able to find some idiot to overpay for your '06 and a dealer blowing out an '08 so that the price difference is minimal I really don't see the point. Remember on a new bike you have to pay freight/pdi/both taxes, work out the numbers and see how much you'd have to fork out of your own pocket. While the S2 is nice and the improvements are definitely a positive. Does the additional money make sense for what is essentially the exact same bike? You're really not upgrading, rather moving sideways and spending a good bit of money to do so
If you have some extra coin in your wallet, why not get a different bike. The FZ is definitely nice, but it is an entry level 600, there is no changing that, there are many bikes build to a higher standard for not much more coin. My pick would be the Speed Triple, much nicer build all around, and there are bargains to be had if you look at a couple year old models.
Maybe I'm just too practical...