They looked similar (same size and same vertical aligning) before Martin made that change to reset.css of moodle2 theme of moodle.org - at least all my browsers show now superscripts as superscripts and subscripts as subscripts... it should be ok.
There are still those font size issues left in moodle.org...
With font tags <font size="6">H<sub>2</sub>O and x<sup>2</sup></font> : H2O and x2
With span tags <span style="font-weight: normal; font-size: 36px; line-height: normal; font-style: normal; font-variant: normal">H<sub>2</sub>O and x<sup>2</sup></span>: H2O and x2
( but this font size issues is another story http://tracker.moodle.org/browse/MDLSITE-561 )