Probably the biggest thing is that the ZX6R is a Kawasaki!! Sitting on the two bikes the 6R is more comfortable, as the ride position is more condusive to longer rides. I think that the F4i has higher pegs, which causes for some cramped up legs!
1. F4is have a well known problem with their CCTs. Honda doesn't always replace these under warranty.
2. The F4i seat is rock hard
3. F4i can't use swingarm spools
4. Single low beam light. ZX-6R lights are much much better. Ride magazine rated the ZX-6R lights as 4th on their Top 5 bikes with bright lights list.
5. F4i could use some more ground clearance
And unless you get a really good deal on the F4i, the ZX-6R will cost less as well.
Sit on both, and ask yourself which one turns your crank.
For me, there's no question... Honda's have never "done it" for me... they always seem too polished and too finished for my liking, and closed in... sorta remind me of a hardcore Katana when I sit on them... and that's NOT a good thing.
But there's likely a reason why Honda can't get enough boatloads of them over to us every year... all a matter of personal opinion. The power and handling on those two bikes will be very comparable.
"Keep yer feet on the pegs and your right hand cranked."
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