The internal transformer hits the main voltage rails with more power than the wall wart, giving the VC6Q a slight edge in sound. Otherwise, they use the same mic pre amp, have the connectors on the rear, and sound almost identical. This boils down to two choices. Can you afford the difference, and will you get use out of the additional controls and features. If money is the only issue, the VC3 is still a great choice.
Some people get two for stereo tracking and mixing to two track.
For the more experienced, the VC6Q offers more control for the user. In our opinion, the VC6Q is worth the difference. The meter in the VC3 is set differently than other meters. The VC3 has 28db of headroom and likes to be run well into the red light. By hitting the VC3 hard, you get more out of the compressor as well.