The Main Scenario dungeons are a different beast entirely. They're a relic of an older game design that was phased out entirely after ARR. A lot of people agree that they need to be either massively revamped or (and that's the option i'd go with) turned into solo duties.
As for Alliance raids, they're pure chaos, and I think that's the result of putting 24 people into the same raid with zero organization. Things can and will get messy.
And regarding the loot boxes, if no one seems to need them, groups will often just run past. No point going the detour if everyone's just going to pass on the loot. I've yet to see anyone complain when someone goes out their way to loot them though. And in post ARR dungeons, you no longer have chests tucked away in optional rooms behind an extra pack of mobs, everything's accessible.