All the shiny, new features will be put into the Drupal 6 versions, but if there are any bugs that need fixing in 1.0 (and I know of a few already), they will be taken care of. I suspect Ubercart 1.1 or 1.2 will be available by the time 2.0 goes out the door. We'll try to keep the bug fixes in sync as much as we can, but that will become less necessary and possible as the branches diverge.