There's no disadvantage to VR other than a little bit of added weight. But (at least in the Canon camp) it can be disabled if you want to induce some blur or shake.
As for which one is better (if you can only have one) I think it depends on your usage...
18-55: Would be your indoor lens, and VR might help you use a longer shutter speed to avoid using your flash
55-200: At the longer focal lengths, lenses are more susceptible to small movement
So which will you be using more?
