In my experience with Drupal over the past few years, it's best to be one major version back, at least until the new version has been out 4-6 months. This gives everyone time to catch up and get stable. I wouldn't even consider building a complex, 3rd party module dependant, site on Drupal 6.1 at this point. Drupal 6 has only been officially out for a month! You will find too many modules aren't ported or stable. With PCI requirements and other concerns, shops need to be stable and secure. Bleeding edge is not a good thing for shop sites. Also, many existing Drupal site developers wait a bit to upgrade all of their sites -- for stability reasons, and it's just plain tiring and not something that you do lightly or quickly.

I think it would be a very good idea to focus all efforts on getting Ubercart 1.0 out the door. The port to DP6 will be much easier as well if taken from stable code. I'm not suggesting waiting until every bug is fixed -- that never happens anyway.