Update, there is an active real project doing much of this: http://drupal.org/project/variable
This is primarily a matter of deployment and developer sanity, but it is also a performance issue: large variables that aren't used on most pages shouldn't be loaded on every page.
The variable table has to change, and we need to distinguish variables that are needed on (most) every page load from those that clearly are not.
Except where otherwise noted, content on this site is licensed under a Creative Commons Attribution 3.0 Unported License.