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Kind of like Xrayz0r is that it would have to be on the after effect. The entire basis of the core Sharingan ability is the enhanced ability to discern pretty much anything.
That is to say, that Sharingan makes eyes work to their fullest (which is why a regular sharingan tires Kakashi out). With an Uchiha body, the Sharingan is to be less draining (probly meaning that they suffer no natural drawback to the strain on using their eyes to such an extent).
However, Mangekyou Sharingan is not like the normal Sharingan, as it not only allows the new abilities, but as we saw from Itachi grabbing Sasuke's arm that had the Chidori in it, and when Sasuke was fighting Naruto, it notices even more, making the eyes surpass their limits. This strain while at the start would be an effective advantage in the battle, in the end, one is left so strained and exausted from the ordeal that the biggest strength is initself the largest weakness.
We might surmize that because of continual pushing the limits of their eyes that they can degrade how well their eyes will work, and concurrently how well the MS will work from then on in the future.
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