The new form API has some terrific features for Ecommerce. Specifically, I think the checkoutapi can be fully removed. In its place, we do one form with #multistep = TRUE. Default ecommerce will have a couple pages in that form just like we do today. Contrib modules that want to hook into checkout do so with hook_form_alter(). Seems cleaner IMO.
There are probably other opportunities, but that one jumps to mind first.