I own both lenses and they are both among my most used lenses.
My perception is the MP-E 65 may be a tad sharper at 1:1, but if you are trying to compare these lenses at all then you are asking the wrong questions. These lenses have completely different purposes.
You will almost certainly need the MT-24EX with the MP-E 65. The vast majority of my shots with it are handheld and you will need this flash to get anything with it. In terms of whether you will need a macro rail and tripod, that depends on what you are shooting. Macro rails and a tripod are really the domain of abstract work or focus stacked closeups.
Personally I own a pair of RRS macro rails and a Gitzo Explorer-type tripod. I use them far more with my 100 macro than with my MP-E 65, and on the rare occasion I use them with my MP-E 65 it is with a Cognisys Stackshot in order to handle the DOF issue.
For insects and drops of water, however, you'll be shooting hand held most of them time so you'll just need an MT-24EX.
Still, if you are not familiar enough with macro I advise you to stick with the 100L because the MP-E 65 will just frustrate you.