Things like the inventory are just plain bad. It has nothing to do with arma2 being a milsim, it's just a bad inventory. Things like not being able to turn around in a doorway without the rist of shattering all your bones is the fault of the arma2 engine, and again has nothing to do with it being a milsim... it's just bad. The reason people can join a server and press a button to explode every other player connected is because Arma2 lets clients have access to the server via scripts. You can pretty much do anything you want once you're connected to a server, including spawning anything, turning players into farm animals, teleporting, etc. Again, this is a problem with Arma2 and nothing to do with it being a military sim.
The zombies AI is because Rocket just used the panicked civilian ai because he wanted it to be difficult. AFAIK he also increased the speed of the zombies to the point where servers have a hard time keeping up with them, which is why they're prone to teleport around.
The inventory wasn't designed as an RPG inventory, which is how DayZ tries to use it. It's usually only used as a loadout screen when buying gear at base in ArmA 2, and virtually everything in your gear is supposed to accessible when playing without ever looking at your gear screen. It's not bad when used in its original context, but it wasn't designed for the full functionality required by an RPG. It doesn't handle backpacks, food, water, and giving stuff to people well because it was never intended to.
I've never seen the doorway problem in ArmA 2 under normal play (and I have about 150 hours into it), so I can't comment on that. Ladders are definitely a problem, but I can count the number of FPSes I've seen that do ladders well on one hand. They're a classic problem.
Security is a big problem. I don't know what the deal is with BattleEye not working well, but it doesn't. Again, however, it's not a problem unique to ArmA; most online games I've seen have at least some problems, and games run by smaller companies like Bohemia Interactive tend to fare worse.
The other thing I see get a lot of complaints is the menu system. The menus were designed so you could command your squad off just the function keys and mouse (select units with left hand, scroll to command with mouse wheel). DayZ has no squad functionality, which leaves the scroll wheel menu as an irritation. It just wasn't optimized for swapping personal items.
KG