I've actually owned both, so I'll throw my $.02 in here.
The Buell is faster; has better suspension; stops better; shifts better; has more room for a passenger; has a more comfortable seat; parts are cheaper; and maintenance is limited to basically oil changes and spark plugs. If you like effortless power wheelies, the Buell is the one for you. If my experience tells me anything, the Buell will be at least as reliable as a Kawasaki of similar age and mileage. The few typical XB Buell problems are well documented and easily fixed.
Annoyances? Sure. If you're inclined to ride in casual clothes (jeans etc.) you will feel the heat on your right leg. The headlight sucks. The rear cylinder has a cooling fan that is pretty noisy. The fuel "tank" is too small for touring, even though gas mileage is quite good. The dealer network is a joke, and even though they've come a long way from the tube frame days, Buells still seem a bit home-built in their overall state of refinement (some may say that's a plus, YMMV).
If I was going to get another Uly, I'd get an '08+ because there were some significant upgrades, including increased steering lock, an improved EFI computer, and a better oil pump. And, there is the rub. An 08+ Uly is going to cost $4,000-ish more than a new Versys.
I want to be clear that I think the Versys is an awesome bike, and I love mine. There are some areas where the Versys is better than the Buell, including fuel mileage and range. I actually like the overall size of the Versys better; you can use a (small) magnetic tank bag; and there are more Kawasaki dealers around.
It's not really a fair comparison because the Buell is a much more expensive motorcycle. The Versys is sort of like a mini Uly that's 90% as good and costs 60% as much. If money were no object, I'd probably pick a nice '09 Uly, but I think that the Versys is a better deal for the money, and in the end you'll be better off with a new Versys than an '06 Uly.