The early 7th gen VFR800's with VTEC had some issues ~ a couple of wiring harness fires, and some bikes that seemed to have a harsher VTEC transition from 2-valve to 4-valve operation.
I rode one in 2003 and it had what I thought at the time was fairly harsh vibration above the VTEC transition, which was fairly abrupt depending on whether you were just approaching it slowly or throttled through it quickly.
The next I rode one was in 2008 and it had neither of these problems.
Most people over on vfrworld.com and vfrdiscussion.com will tell you the bike got properly sorted it around 2006:
Honda VFR800 VTEC (2005 - present) review - Sports Tourers - Motorcycles - Visordown
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Overall, the bike is definitely a more refined product than the FZ6R, with more power for 2-up riding although I have not seen a lot of people travelling together on one.
Since the FZ6R never had ABS, and it was an option on the VFR, I would hold out for an ABS model. It's the one thing that truly makes the 2006+ VFR800 better.