A legitimate list, but I propose a different perspective:
What you list as being the biggest annoyances is one of the most endearing features of the game, IMO. Just about every other video game gives you ultimate and total control over every aspect of your units. Units in Dwarf Fortress treat your direct commands as 'strongly suggested'. Most of the vaunted difficulty of this game springs from this misunderstanding of how your commands will be carried out. Once you figure out that bit, everything else starts to fall into place. You are not here to control the dwarves, you are here to prod them in the directions you would like them to go. Even the message you get in Legends Mode when retiring a fort bears this out: "At [TIME] [GROUP_NAME] of [CIV_NAME] at the settlement of [FORT_NAME] regained their senses after an initial period of questionable judgment." You, the player, are not a deity in direct control of your thoughtless minions. You, the player, are the nagging little voice whispering in the collective ears of the dwarves, who are trying like hell just to live their lives and not succumb to the idiotic desire to build a massive magma moat around the fort, replete with self-powered pump-stack magmafalls, for the mist, and then a solid gold throne room underneath with trap doors and pumps, in case the mayor makes too many demands, and then...
I agree in part — this was highly endearing to me for my first dozen or two forts, but it eventually lost a good portion of its charm, especially when it’s for STUFF YOU HAVE TO DO RIGHT NOW, like lofty mentioned; building walls and pulling levers
I can live with the broker taking forever to go to the depot and the station command being next-to-useless but a dwarf eighty z-levels down who was just pumping magma being assigned lever-pulling is an absolute pain, especially when the lever is to pull the bridge up on the only entrance of the fort to stop goblins from getting in
edit:
by the way, lofty, I found your criticism and summary enjoyable and insightful to read, I hope you stick you around