Unlike a lot of my colleagues in the field, I stayed with my T3i until I proved myself worthy of an upgrade. But now that I decided to get a "better" camera, I am finding that spending more money means I am getting less performance. Why is that? I decided to buy a Pentax K-3, but eventually returned it because it did not give me the flexibilty I wanted. I decided to put off buying another crop sensor camera for now, so I bought a 6D with a 100mm Macro L-glass lens. My old T3i with a Tamron 28-300 zoom still produces much better images under the same conditions. What gives?
Your images don't contain EXIF data and since I'm not there to see what you're doing, I can't say for certain why you're getting these results. I don't own a 6D (though I do have a friend who owns one and it seems to be working extremely well for that friend), I do have the same EF 100mm f/2.8L IS USM lens and I get consistently good results. If for any reason I do not, it will be because -> I <- botched the exposure... not the camera.
The camera neither gets the credit for my good exposures, nor the blame for my bad ones. It's like blaming the hammer for building a bad house. It's not the hammer's fault.
I did not invent the rules of exposure nor the guidelines for composition, minimum shutter speed to focal length relationships or any of those helpful guidelines. The credit for all of that goes to many photographers who came long before I was alive. But I do know that when I follow their guidlines, my exposures are improved.
Here's one example:
This a typical example of what I expect to get with the lens... there are many others... but this was taken at ISO 100 and 1/100th.
IS was on but the caution here is that since this was ALSO taken at f/2.8, the depth of field is extremely shallow so once the camera locks focus, the tiniest movement of my body either leaning forward or back by perhaps just a tiny amount would throw off the focus. For this reason, close-up photography and tripods... pretty much go hand-in-hand. So while I do have examples taken at much slower exposures, they were taken with the camera on a tripod and I was using a remote shutter release.
There were two true statements posted here.
One was, " I'd believe a lot of nonsense." I'll bet you do. 
And, "I know the rules and in this case things do not add up." Yes and until you start a systematic plan for elimation of what is wrong, things will never add up. Do yourself a favor and try the lens tests, please! Find out where the issue is.
