I've been playing DF for about a month now, and the biggest irritation to me is the path finding algorithm for (most noticeably) stockpiles. (I know there's a lot of path finding discussions, but I haven't had time to read through the hundreds of pages of suggestions, so if this has been covered, forgive me.) It appears to me that Dwarfs don't take any obstacles into account when trying to place items into stockpiles. They simply pick the closest stockpile, disregarding walls, floors, etc., to the item. For example, whilst tunneling under a mountain (side view):
#> A B
#X########
#< o#
##########
A dwarf picking up the stone 'o' will haul it to stockpile B because it is only 'two' steps away, even tho the Dwarf must carry the stone
over stockpile A. This drives me crazy, and seems to negate any purpose of traffic designations. This problem may exist in other path finding, but is made obvious by Dwarfs carrying items over the stockpile they should be storing them in. Also, Dwarfs will place items in the free stockpile square 'closest' to the item they picked up, resulting in items being shoved all against one wall, even when (for example) the access stairway is in the center of the nearly empty stockpile.