Perhaps we need to come up with some mechanism for the theme to name those regions, and have that name show up in the block admin page. Thus, most existing themes would in fact name them "left" and "right" but some other theme could name them "region 1" and "region 2."
At a minimum we need to consider that eventually the block admin page is going to have to deal with blocks which will never end up on the "left" or "right" of the page, and thus using those terms will remain confusing.
The big roadblock for custom theme regions is having multiple themes per site. This is a valid use case (sections.module, or even a 'mobile' theme for PDA/Cell phones). I'd suggest you check out some earlier discussions on this in the archives. Steven Wittens