I rode both (2011 models) and definitely preferred the Z. The Yamaha wasn't as torquey, had more vibration, a tall, hard seat, and in general felt a little more twitchy over bumps. It was still a nice bike, but to me the Z was just "a bit better" in every way. Plus the FZ is a little long in the tooth style wise and the Z looks bad ass. The FZ didn't have much personality to me, where the Z has a vboost like "hit" of power in the upper midrange that lofts the front wheel with ease to a huge top end hustle. Plus you got a great intake howl when you opened it up.
The Ninja 1000 is more similar to the FZ1, though mechanically it shares a lot with the Z. Little more relaxed posture, shorter gearing, more fairings.
Overall the Kawi is just more fun, more for hooligans, where the Yamaha is more "mature" in feel.
Said it before and I'll say it again, the z1000 is the bike the gen2 should have been.