My suggestions are the following:
-Please, PLEASE, fix horrified merchants having caravans explode and just disappear. This bug has been around, literally, for years. I usually settle in evil regions, so evil rain is pretty common. I usually build an underground tunnel as close to the edges of the map as possible, so I can force caravans to come through a specific spot, but I can't really build any cover for them on the 5 or so tiles they spawn to protect them from the environment. At least, the addition of some sort of "tent" building for map edges could help alleviate the issue. Also, sending actually capable enforcements with the caravans would be good. Please, make them stop exploding and being scared of everything. Please.
-Make stockpile options more user friendly. Split boxes and bags into different categories, Would be nice to have a containers stockpile, so the furniture stockpile could get a little less uncluttered. Also, stuff like large tools and other tools could be split into specific categories. I assume it would not be too complex or time consuming to implement this, and it would improve things considerably.
-I would love to see workshop zones. Using cabinets to store raw materials close to workshops, allowing to set desired material on cabinet X, and have the crafter prefer the stored materials to stop him from walking 100 floors to pick up a single stone. Allow haulers to bring heavy materials to the cabinets using wheelbarrows. That would work wonders and would make stockpile linking much less annoying. Regarding customization, having a workshop zone where, for example, you could encrust whatever came out of another shop in the same zone would make encrusting less of a hassle.
-Have a building for stockpiling finished goods/armor/weapons/trap comps/etc. Instead of making 9 bins for a 3x3 square, simply allow the building of some sort of big container. That would alleviate the bin bug issue too, since I believe it is a bit more complex of a bug. (using this building in tandem with workshop zones would be pretty neat too, instead of cabinets, for raw materials, depending on material size - cabinets for thread/clothes/small stuff, big 3x3 locker "workshop" for stone/bars/big stuff?) Please bear in mind that, imo, this locker should store more than a common stockpile, to incentivize its use, since if it stores only as much as a stockpile it doesnt really accomplish much.
Cheers! And sorry for the bad english.