Ok, this thread is sounding exactly like the forums for every single bad beta test I've ever been in. "WTF this sucks what were the devs thinking putting it up like this" "IT'S JUST A BETAAAAAAA IT'LL GET BETTERRRRRRR" and then it doesn't because the beta tests actually do usually turn out to be pretty close to the final product and all the "just wait it'll get better" people slink away never to be heard from again.
For my part, I can see how the military improvements could be better than the previous system, but it also overcomplexifies things. Sometimes you just want a woodcutter to take his axe and go smack some beasties who are scaring the fisherdwarves, without going through all sorts of paperwork involving who's allowed what equipment beforehand. Until that becomes possible, it's more of a hindrance than a help. I don't WANT to have to set up training sessions and barracks and duty rosters and so on, I just want "You, you, and you, grab a weapon and go stand guard there until I tell you otherwise". The current military interface completely gets in the way. It makes difficult what should be easy. Until that's resolved, it's a problem.
The caverns and so on are a net plus but it wouldn't have taken that much to add them to 40d. The materials and layers system, I have not seen any evidence at all that it was worth all the time. Lots of really odd bug reports and claims that it's just that the raws aren't set up right yet, but until I actually see results where the raws are set up correctly and it works right, I'm reserving judgement. 40d worked fine in that regard. To the point where I've been wondering to myself what it would take to do a rollback to 40d's system and just tack on the caverns.
In short, it's not at all clear that this IS the right track for the game in terms of fun and functionality. And yes Toady will do whatever the heck he wants with it. But open discussion of the issues people have can only clarify the situation.