1. Release early, release often.
You often say that donations are better in release months. People like releases. Is there a compelling reason there cannot be a Dwarf Fortress release when the underground features are finalized? Why couldn't there have been one before that section of work started? Especially 7 months since the last release there should be another release before the save compatibility is broken. Is the gain of not releasing sufficient?
2. Include a few community graphics packs in the official download.
The largest problem I had with the game when starting was figuring out what was what. I almost immediately switched to the Mayday graphics pack and have not stopped since.
Keep the official graphics as ASCII, but also provide a popular selection of other graphics packs in the official release. There should also be an in-game way to switch between these sets so people have easy access to that.
3. The lag monster, as someone in the thread termed it.
I'm not talking about multi-threading. Once your fortress reaches a certain size in dwarves or items the frame-rate takes a nose dive. I have a 1x1 fortress with 128 dwarves running at 7 FPS on an Athlon 64 X2 4200 and it even has a magma pipe in the center taking up most of the space. Algorithms that work great with 10 dwarves in the beginning break down horribly later.
Let us supply game saves that you can profile to find the spots making even the most powerful computers crawl. This isn't a total optimization of the game but finding and eliminating the top 2 or 3 worst abuses of time to give us a little relief. (Ever tried viewing "stones" in the Stocks screen with 238,000 of them? Or even waiting 10 minutes for "Cleaning game objects" with that many?)
4. Tasking
I once had two doors that refused to budge from the ground in my fortress. It took me weeks to realize that the doors wouldn't move (or dump) because they were tasked for building but it was suspended because some dwarf was walking through the door square when another dwarf tried to hang the door. In fact, there's no way to know how many things are currently suspended except by remembering what you have tried to do and noticing. The announcement message is nice, except that you can miss it or forget, plus the message doesn't give any hint as to where the building was suspended so you have to go figure out which one. Even a blinking red background on the items tasked and the building spot suspended would help some, especially if the item tasked could Zoom to the building spot. Also, tasked items should be allowed to be moved for other buildings on that spot, otherwise that square is off-limits for any future building until the other one finishes.
5. Jobs
Dwarf Manager is essential. Toady may not want to be subject to third party needs or breaking essential tools but it is already too late for me due to the job interface.
6. Stockpiles
I wish there was a Stockpile Manager too, but alas. Ever tried to figure out how many of your stockpiles accept armor? Or how many squares of stockpile are left for weapons? Or how many plump helmets are decaying because you're out of stockpile space? Ever needed to disable seeds from all stockpiles except the current one? Ever had to increase the size of a custom (not the custom template) stockpile and be faced with either wiping it and recreating or trying to duplicate the settings in a tiny adjacent stockpile?
7. Trading
I dread the trade depot. Once your fortress gets larger you're stuck with 100 times <down><enter> or using a third party utility like AutoHotkey. The categories are insufficient so things like prepared food and mechanisms can only be found via the Search mechanism, which re-filters (and thus lags) on every keystroke instead of waiting until I hit Enter or pause typing. Having a mandate knocks out entire bins of goods by default even if only a single item in the bin is forbidden, so turning off culling is essential.
The trade depot move goods screen should use a screen similar to building weapon traps. Key differences would be the items are not sorted by distance, but instead should be sorted by category, then item type then item value. This would be similar to how the actual trade screen apppears, although it isn't quite as neatly sorted. We could mark goods to go to the trade depot screen by hitting + a few times, each time it picking the nearest of that type ("* dolomite grate" or "-=*=- dolomite grate" being separate types, as well as from "- dolomite grate"), or with > letting us increase by 10 items, or < reduce by 10 items, or shift+enter to mark all of that type. Bins should be transparent and not traded to the merchants since we rarely wish to rid ourselves of actual containers.
8. Building materials
Almost always I want to use a specific stone (or block) type when I'm building something. Almost always I have to hunt through 5 to 8 pages of materials to find the one I want because they're sorted by distance rather than alphabetically.
On a related note, I'd really, really like to be able to pick a specific rock to make crafts and buildings out of, an eternal suggestion. If I'm trying to make my bridge out of pure dolomite there's no way I can reliably ensure only dolomite blocks are used, especially if I have active mining going on and thus can't even mass-forbid everything else.
9. Job Manager
Not being able to designate more than 30 of any item or clone an existing request for more of the same item is a real pain. As it stands if you want to collect a lot of sand, without repeat, then you have to repeat the item search multiple times to make a bunch of 30-item jobs.
10. Replace liaisons
It is really tough on trading to lose a liaison because you can no longer request any specific needs. Also a pain to lose a liaison when you become a Mountainhome -- you should be able to make requests still, with it presented as your requests of the lesser forts to provide to the home.
10. Running out of seeds
I once accidentally cooked all my plump helmets because I didn't have enough barrels to brew anymore and I didn't have any seeds until the next dwarven caravan arrived. If I had been a Mountainhome then I would've been in real trouble. Ideally I could set an absolute floor of seeds that must never be cooked/planted/etc. just in case I do lose all the other seeds. At that point I'd drop the limit to let the reserve be used to restart the process.
11. Running out of wildlife
Really makes fishing and hunting not worth it because it cannot last for more than a few seasons. That cuts out a lot of jobs and activities that would otherwise be considered staples of civilization.
12. Wrestlers disrobing each other and then unable to train because of holding armor
Frustrating for litter and productivity.
13. Nobles
Dwarf Manager eliminated my burning hatred for their non-working, space-wasting, useful-dwarf-killing sacks of flesh since I give them hauling jobs now.
14. Dwarves fleeing into enemies
When you are faced with an enemy in front of you and the fort behind you, do not run straight ahead! Or into more enemies to the side! This was especially bad in my 1x1 fort as all the dwarves in the above ground tower would freak out and run out of the building into the unprotected grass instead of heading down the same steps into the fortress proper.
15. Interface
Many people have commented on this so it is redundant. I didn't even know about 'T' for the longest time. When using the unit list, it needs to return to the unit list at the dwarf you viewed when you hit space on that dwarf. Preferably also divide the unit list into separate categories to avoid carpal tunnel page down activity, such as: Dwarves, Animals, Friendly, Wildlife, Hostile, Deceased.
... that should do for now.