As a non-technical reader I agree with all the arguments against this proposal. I do not understand why there is the need for a change but, for what it's worth, here is my input...

If I could change the Shortcodes API I'd want them to fail well. If I remove, or deactivate, a plugin something like [shortcode_name sc_vars1="123" sc_vars2="something"] is shown publicly all over my website in place of the originally intended content. It looks shabby. And with no in-built method of finding and deleting unhandled shortcodes, it becomes very frustrating trying to manage a site with a decent number of posts.

I'd wish for text which meets the shortcode syntax, but for which there is no active handler, to be hidden or some alternative (pre-defined) content used to replace it.

In addition, the ability to easily search for and edit/remove unhandled (and handled) plugin shortcodes would be very welcome.