I have done a series of comparison shots at mid-distances, a wooden picket fence with lots of grain detail, and distant shots at a nearby mountain park. I have done this for all my lenses, on a tripod, self timer, etc so taking my shaky hands out of the equation. I shoot each lens at a range of apertures, using both viewfinder AF, and Live View AF. On those tests I can't see any difference to speak of between the two 100 mm lenses, both are very sharp across the entire frame. It did seem that on my t2i the 100 2.0 would once in a while be just a smidgen front- focusing as I sometimes would get a little sharper on large aperture shots using Live View focusing. When I got my 5d Mk III, I bought a Lens-Align unit at the same time and tested all of my lenses. Both 100 mm lenses were spot on. The 24-105 kit lens that came with the 5D Mk 3, however was off at the long end. Even with AFMA applied to that lens, at 100 it has nowhere near the IQ as the two 100 primes. The 100 2.0 is faster to focus than the 100 2.8L macro, probably due to the lesser total focus range. It is also very quiet focusing. I think you may have hit on a possible explanation for your initial impression of the lens' sharpness - using a pretty high shutter speed (1/250 or more) is what I found I needed to be sure to 'take the shake out' using handheld, which is more than the rule of thumb would say you needed for this lens; ie 1/160th on a crop sensor camera. The shot I attached earlier was 1/1000 second.
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