I love the Ninja 1000, it's a great all around bike. It's exactly what I'm planning to get instead of a 600 supersport... not because it's quicker than a zx6r but because it can be an "everything" bike.
The only issue is that it's tough to get a good priced insurance quote so you really have to shop around.
If you google you can get a rough idea of performance of the bikes (which vary depending on the source)
Ninja 650= 3.8-4.0 sec; high 12s or low 13s quarter mile
ZX6R= 3.2-3.5 sec; high 10s quarter mile
Ninja 1000= 2.8-2.9 sec; mid-high 10's quarter mile
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