A longer working distance from your subject, which generally is good for not working in you own light, and gives you more room for a flash set up. Less chance of scaring the bugs away by getting too close too.
The EF-S lens wont fit any 1 Series body or a 5D if you wanted to upgrade in the future, whereas the 100mm Macro will.
Both excellent lenses. I'd have to say though that the quality and reputation of the Canon 100mm is a given - cast iron guaranteed - five star - gold plated.
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