I'm big Drupal fan, and some very high profile sites use Drupal which also suggests that its a good system. Can the same be said for Ubercart?
I've used it for some small ecommerce sites purely because I know Drupal. It seems to lack some basic features and also relies on javascript. I dont know of any high profile ecommerce sites using it.
My productivity would take a big hit if I had to learn a new ecommerce platform and also if I couldn't use my favorite CMS with it, but do I have a choice? If not I guess I can hope that Drupal 7's Commerce module will be an improvement.