My initial thought on splitting the CSS file was to offer a visitor theme options (kool factor); then came the practical idea that themes may be a way of providing accessability to visually impaired visitors; then came the thought of offerring choices in color contrast if, for instance, my original choice in colors put a strain on an individuals eyes (I have eye issues so these thoughts just naturally bubbled up).
Actually, I only split off the color rules into a different section of my prime CSS file in preparation to creating two files. One for color and the other for topography and layout per the book I recently completed, DOM scripting.
The most visable downside to this method IMHO is maintenance. Each time I encounter a problem with the presentation in a page as a result of CSS or if I want to change or remove a rule then I need to be sure to search for two possible rules in the CSS file, one for color the other for layout and topography. The benefit, for me and my admittedly small number of less than one hundred pages, is nominal, but I'm just guessing. Maybe webMasters with thousands of pages have a different view no doubt. Still, apart from whatever technical value the splitting may allow, the process of not being able to complete the CSS shorthand properties in one place and having to search for more than one rule for the same selector was becoming frustrating.
In my frustration I started looking for a better way(a way out without feeling guilty). So off to w3.org I went. Here [w3.org ] describes how a visitor can alter a web page. So I rationalized that instead of me deciding the theme or trying to make a determination on all the possible colors or contrasting attributes that may provide relief from eye strain, let the user decide (aka passing the buck).
I have not tested this, but I can see that IE [windows.microsoft.com ]
allows text and color changes and even allows user to add a user stylesheet.