I initially had a problem with my quadrotor flipping on takeoff due to the ZeroTheIntegral no being set. Since I did not change this myself, I suspect the problem is that this was not set in the profile I used when I ran the vehicle setup wizard. Since there is no guidance given in selecting a profile, it seems like this can lead to lots of frustration for new users if they select a profile that is not well behaved. It might be useful to have two levels of selection here, known good setups for beginners, and use-at-your-own risk setups for advanced users.
Also, the orientation of the FC is not accounted for in the Wizard, and requires customization if you don't use the correct (but non-intuitive) orientation. An additional step here would save novice users a lot of headache.
I suspect most people assume if they use the wizards, they should be able to get their machine off the ground; these two issues can easily prevent that from happening.