I agree its over rated as well, however I think people buying a card should be aware that the framerate values are an average over a given time, not an instantaneous thing. So with stuttering of any description (whether it be microstuttering or other types of stuttering) 60fps can easily "feel" like 30fps. You're buying an expensive card to get a higher framerate when in reality its not effectively going much faster than a single GPU option.
It doesn't make much difference at higher framerates, but when you end up eventually playing games with 20-30fps when in reality it feels like 10-15fps, that's when you really start to notice it.
At the end of the day the framerate shown by programs like FRAPS is secondry to having a smooth playing game. Regardless of whether you have a single or multi GPU system.
You could always disable SLI if it bothered you enough in a game. Although then your framerates would drop. I've never noticed Micro stuttering.