First, I think Robert Chapin and others involved in this effort deserve a real round of applause for taking on the increasingly complicated and unsustainable shortcode system now in use. These are the kinds of issues that are must fixes for the longer term, but rarely result in much glory for the effort.

That said, I really think the solution needs to be a completely new feature that replaces the shortcode system altogether, one that is awesome enough to create incentives for developers and users to drop shortcodes in favor or the much improved alternative, while maintaining support for the current shortcode feature for some defined period.

I think that would also prevent users from potentially getting confused and suffering errors, developers from pulling their hair(s) out at the thought of being forced (you know devs, they hate being forced to change anything they don't absolutely have to), and innovate WordPress by a leap in the process. I hope that makes some sense.