I've never been too bothered about dwarves not naturally saving empty barrels for alcohol. Stuff like that is part of the appeal of the game for me. It's possible that your farmers/cooks/butchers kept snatching up the new barrels for foodstuffs.
There are bigger micromanagement annoyances to me than that, most of them likely due to bugs. Planters, for example, will no longer stop planting seeds if it's too late in the season to grow that crop. You now have to watch the date yourself and go in and change the fields to fallow at around halfway through the season because if there are still seeds left to plant your dwarves will happily keep planting even though it'll all die at the season change. I discovered this when all but two of my rock nuts disappeared on me when Autumn changed to Winter once.
Another example is military equipment. At the moment dwarves have a hard time picking up the right stuff or simply dropping their stuff on the spot to pick up different stuff. The only solid solution I've found is to assign each individual soldier specific items so that there's no ambiguity. Only problem is that once an item has been assigned it doesn't disappear from the list of available items and if you assign the same item twice, the first soldier drops it off his list. Forbidding removes it, though, so I have to fiddle around with pausing the game, forbidding all pieces of that gear, going into the stockpile, unforbidding that one item, assigning that item to a soldier, reforbidding the item then unforbidding another, assign THAT item to another soldier, etc.
I like micromanagement sims just fine, else I'd not be playing Dwarf Fortress. However I do agree that some stuff, especially the workarounds for bugs, really need to be fixed.