My experiments so far have yet to find a place where the YUI css actually has any effect. I've not yet found a way to simply not load it from within a theme though. I've deleted it from core Moodle though and not been able to tell the difference. (To be exact, the default font changed, but if your theme sets the font then you won't notice).
Comparisons and advocacy
Moodle 2.0 vs EDU 2.0
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