I'm always surprised when I find out how much trouble people have with the military interface- I've found that the basic premises behind it were rather intuitive, and a little dedicated work irons out most of the quirks with the system. I've always had more trouble with farming and maintaining the clothing industry- I can never quite balance it right.
There are some fundamental issues:
1) Schedulle switches do not provide feedback. It takes some time for dwarves to snap out of their previous orders. It makes everything seem like it just does not work at all. I completelly expect squad that was just assigned to patroll duty to actually start patroling instead of chilling out for month or so.
2) Enter key deletes. Seriously, how come, that is like ... worst key posible for that task. This is especially annoying when you accidentally delete chest item from default Metal Armor as there is not way to re-add that one other than reseting uniform... and if you manage to delete that from uniform, well it is ctrl-alt-del time and continuing from latest backup.
3) Squad assigments forces you to pick for all the dwarves,
including other squads. Cue massive confusion and accidentally canibalized older squads. Even worse, when you add dwarf, list scroll position resets and if you want to add another dwarf that was right next to him (typical for new immigrants), you have to scroll again. It is also painfully useless if you decide to draft everyone as emergency response - try doing that to 150 pop fort without going insane.