The YUI Library resets the sub/sup tags vertical alignment (forcing the text inline with normal text).
The vertical alignment needs to be set in the base theme for these elements so that they appear as one would expect on the page.
Problem: When setting text somewhere to use subscript or superscript, it looks correct in the TinyMCE editor, but once you are viewing it outside of that on a page, the sub/sup'ed text is forced vertically inline with the other text.
Expected: The sub/sup'ed text to be slightly lower or higher than the rest of the text (effectively increasing the line-height as well).
Attached is a small patch which adds two css rules to the base theme to set the tags to their expected alignment.