The lack of a civilian alert is a pain
I actually prefer the new burrow system and the fact that it's now unattached to an alert system.
I mean yes, once you have a large population, it's still a grind having to assign dwarfs manually to burrows But the simplicity of just turning them on or off with the pause button makes it a lot easier than dealing with alert schedules.
I've assigned all current Dwarven kids to a permanently ON burrow meaning the never step outside, while all other citizens are assigned to a paused "HOME" burrow. When I unpause it, all adults run inside, allowing the military to do their thang.
Although, the last Vile Force that arrived scarpered as soon as I issued the kill order, so I think the reputation of my steel-clad psychos has travelled.
Edit:
While I've not got quite so many hours in yet (I'm at 69 dude!), my biggest bugbear is list filter limitation and search consistency.
Different lists have different filters available, some have no filters at all (most irritatingly, the trade interface), and Search is sometimes not present, or if it is, sometimes doesn't work.
For example, I'm now at the stage where all "Finished Goods", the staple of my trade economy (bracelets, crowns, rings etc.), are automatically stowed in bins. This means they no longer appear as a category of goods to move to the trade depot, so I have to select bins and individually tick off each bin that contains finished goods or even worse, the goods themselves (because, as noted, when I search the list of bins for "finished goods", even though many are labelled as such, the list doesn't filter out non-finished goods bins).
I understand the drive was to simplify the user interface, but it's gone a little too far and a little too illogically for my liking at the moment.