I've had both over the years and ridden a few more that belonged to dealers, I would say neither is the better bike, they are just different. From nearly 20 years of running dealer ride outs, trips abroad, open days etc I've found the biggest influence on how a bike goes, feels etc is the rider, there are very few bad bikes any more.
I've just returned to the foccer fold after buying a bike to do track days and moto gymkhana, I looked at both FZS and FZ6 and only chose the FZ6 over the older model because a minter came up at the right price. If I'd found a really good FZS first I'd have bought that first.