I never rode the FZ6, and only recently purchased the FZ6R, so I can't make a direct comparison. I can say that I have yet to feel like I don't have the power I need from the ~65 HP from the FZ6R engine when I'm getting around town. As an owner of a CBR1000RR, I can say with some confidence that the only real benefit to a ridiculous amount of power is when you're already going over 60 MPH, and unless you're doing a ton of time on the highway, then this *should* be a non-issue. And if you're doing a ton of time on the highway, you probably should be looking into a different style of bike altogether, like one with a real windshield. Yeah, I've enjoyed blasting off to 100+ mph for short bursts of time on supersports, but it was most definitely just pointless entertainment.
I bought the FZ6R for a few reasons: solid engineering, good power in a realistic range, good mileage, nice looks with an easy-to-remove fairing (*much* easier to deal with than the nightmare on the R6), and a platform that makes it nimbler and easier to control than a cruiser while still having a comfortable posture. I'm satisfied on all counts.
If I could snap my fingers and have my garage magically plop a different bike into my garage whenever I wanted, then sometimes I'd be riding the FZ6R, other times an FJR1300, other times an R1. Life would be great!
Unfortunately, as that isn't an option for me, I had to pick the characteristics that mattered to me at the best price. The FZ6R really hit the sweet spot. Sure, better suspension would be neat to have, but in 99% of my riding time I wouldn't be able to tell the difference. Sure, more power when I'm already doing highway speeds would be cool, but the trade-off for that is usually a rougher power curve and worse mileage.
So basically, I think that complaining about the power difference between the FZ6 and the FZ6R is missing the point. The engine on the FZ6R makes sense for its purpose, as do the rest of its parts, and by all accounts the overall package is a great deal. The FZ1 is still there and very popular for a more performance-oriented street bike. If anything didn't make sense, it was having the FZ6, FZ8, and FZ1 all available at the same point in time. I still don't really see the point in the FZ8 right now. If they dropped it down to just the FZ6R and the FZ1, I doubt anybody would be unhappy with those choices for street bikes. Personally, I'd slap a practical fairing on the FZ1 as well, but that's probably just my preference as a software developer for keeping things clean!