1) Make the default name for squads "Squad 1/2/etc" instead of a random name such as "The cloisters of farting" and allow us to rename squads. The renaming is nice and it makes managing a larger military more easy.
2) Allow us to specify from which side a construction will be built. Dwarves often close themselves into corridors or shafts when sealing them. There is a workaround but it only works when there are no constructions in the shaft/corridor.
3) Change the "Urist has grown attached to a copper short sword" feature to be less annoying. Let us remove said copper short sword in a simple way (without the contortions that are currently required), at the cost of Urist getting an unhappy thought. Personally I wouldn't mind seeing this feature killed but I suppose some may like it for its flavor.
4) Make it easier and thus faster to breach aquifers by lowering the flow rate of aquifers. It just takes too long currently. Alternatively, a "dam" building that can be constructed directly into a water tile would be interesting and open up some ocean fortress possibilities (that don't involve obsidian casting directly into the ocean).
5) Order the rocks in the stockpiles menu alphabetically and add "Magma-safe" to their description when appropriate.
6) Let us specify which rock masons and mechanics use to build their things.
7) Make nicknames of dwarves not be overwritten when they gain a combat name.
Lye and milk should be stored in barrels rather than buckets.
9) Fix the excessive size of body parts causing them to clutter up a workshop.
10) Merge a few of the less used jobs. Animal Training + Animal Care = Animal Handler. Fish Dissector + Small Animal Dissector = Animal Dissector. Metalcrafting + Blacksmithing = Blacksmithing. And a few more.
11) Disallow booze cooking.
12) Reduce value of cooked food and drink. They should only be valuable with (several) high quality ingredients.
13) Reduce the value of trap components.
14) Add a tavern building. Dwarves should drink in a tavern, not in the wine cellar.
15) The mead industry isn't a truly viable source of alcohol because it takes so long for hives to grow and they yield relatively little, while needing replacement. I know it's realistic having to replace hives but in its current state there is little point in making mead. Why have a mead industry when plants provide more, more reliably and don't need constant micromanagement?
16) The milking/cheesemaking industry has similar problems of requiring a lot of micromanagement for meager gains. It's more a curiosity than a real way to provide food to the fortress.
17) Shearing/spinning industry also has similar problems.
18) I miss underground rivers/pools, bottomless holes, deep chasms and giant cave spider nests. I would be cool to bring them back in some form or another. What I essentially want is having more possible unique features that an embark zone can have. The caverns are relatively predictable. How about some chasms in which giant cave spiders spawn? Imagine taming them and setting up a giant cave spider silk farm (which could be made into resilient silk used for armor).
19) Make ponds have ramps that dwarves can use to escape if they fall in.
20) Make magma forges dangerous to use by making fire imps more aggressive and letting them pass through fortifications or something like that. Essentially I feel that magma forges should have some drawback other than being more time consuming to set up than normal forges.
21) Danger rooms are an exploit and should be fixed. It only takes a minute to reach legendary fighter status with them.
22) Mail armor and breastplates should use the intended amount of metal bars to make.
23) Let us engrave constructed walls.
23) Let us construct on constructed floors.
24) Idea to make Vertical Bars useful. Make them a construction (so that building destroyers cannot destroy them) and make them require weapons grade metal. Projectiles can be shot through with no penalty. Similarly, floor bars should act like an indestructible floor grate and also require weapons grade metal.
25) Make clothes made out of resilient materials not degrade. That includes adamantine and maybe giant cave spider silk?