Mil/Mil is also very popular due to the ability to have large elevation changes in two digits rather than three. For example lets say your come up for 800 yards is 28.8 MoA, you're mil hold is 8.5. If you're doing something other than slow firing on the range, a two digit number is likely to be easier to remember.
The_Next_Generation: I agree that it's easiest to use a system that has a matching reticle and turrets, but I don't think it's a must have IF you practice with it.
As to why the military stuck with a mismatched system, I have a few theories. It is certainly workable (it's actually pretty easy once you learn the quick formulas), and there is a ton of publish knowledge on how to do so. My best guess: A mil reticle provides commonality with other MOS that measure things (like artillery and FAC's) so they can communicate with them, and it also means you can use the same syllabus to teach from for ranging. Also the Army uses meters for it's ranges (no clue why) so mils make perfect sense there again. The army in FM 23-10 (the sniper field manual) that 1 MoA at 100 meters is "about 1 inch." So they just neatly sidestepped the majority of peoples issues with Mil/MoA compatibility, as the elevation adjustment was only 1 MoA it makes sense to not worry too much about the lost precision. This approximation is only off by about 2" at 1000 meters.
Also people make a big deal about having to convert between Mil/MoA if you're going to use the fall of shot to adjust off of. Using the above approximation I can adjust off of whatever my spotter tells me. ".5 mil right" I just hold over 1/2 mil or dial in a half minute right (actually .6 minutes, but close enough), "3.5 minutes right" I just dial in 3.5 minutes (7 clicks) of right windage or hold over a hair under 1 mil. Obviously if you both have the same reticle like a sniper/spotter pair would have, it's really a non issue.
-Jenrick