Page Updates and Refreshes
The usual solution to that is to have a lean, user-friendly settings page for the average user and some sort of hidden expert settings (think about:config in Firefox). MediaWiki already sort-of has the latter through the user js subpages; it only requires a bit of thought to make sure the timer objects or the configuration constants controlling them are available from global scope (which is usually easy with jQuery's wonderful data function).
I don't think that's necessarily a good idea. It's typical of open-source projects because it's a concession to anal users :-)
I would take umbrage at that remark, but it appears that MediaWiki does not have high expectations for civility. If thought-terminating clichés such as "crappy" and "anal" are characteristic of decision making at MediaWiki, notwithstanding smiley faces and quotation marks, it would go a long way towards explaining the perception in some quarters of a disconnect with Wikimedia user communities.
I cannot imagine a world in which I would design a preferences system like "about:config."
Preferences are the enemy.