I've been playing since it was released, and these are some of my most immediate thoughts;
1. Staircases! I'm sure it's been said but people aren't kicking up nearly as much of a stink about it as they should be. Removing the ability to dig or construct up, down, and up-and-down staircases makes it impossible to construct certain things, and is confusing and ultimately destructive. Being able to lay out a vertical column of staircase all in one go is great, but it's often the case that a careless ramp removal will, for instance, chop the middle out of a staircase and from then on it's basically impossible to dig up from that point. Not to mention, when you dig down to the caverns, it's a mess to try and seal off the bottom now, especially since hatches are no longer indestructable from below.
2. The replacement of the military screen omits a few important functions, most notably the ability to design a uniform before your first squad is created, and the ability to easily edit a uniform on the fly. This is a horrid oversight. I know some people don't like the old military screen present in .47 (a lot of people left DF when it was introduced) but it was perfectly functional, with keeping equipment, uniform, positions, schedules, provisions etc. apart. I don't even know how to set provisions now and uniforms are a hassle. Please give us back at least all the functionality of the old military screen! Additionally, having nested menus for material selection would be great- for instance, for some reason when selecting an iron shield, 'iron' is hidden somewhere between every kind of wood and a bunch of weird metals you'll likely never see. But, at least this is as functional as it was before!
3. Single right click to exit menu is really annoying. I can't tell you how many times I've spent ten minutes checking boxes in the trade screen before pushing the mouse up and having my hand touch a cup, inadvertently clicking the right mouse button and undoing all my effort. Very annoying. Switching it to a double right click to close, or adding a confirm exit window, or just changing it to a little X in the top right corner of the window would be greatly appreciated!
4. It's not possible to sort potential suspects on the justice screen, (although they are sorted by certain categories already) which means you have to manually go through the list to find a named individual, frustratingly with the name in their local language, when their surname is in English on the report screen. This is extremely tedious and fiddly. Being able to filter out dead people and animals would be a bonus, and also the ability to sort the list by name and residential status would be helpful, and being able to see their names in English and their native language would be helpful, too. Or at least this should be consistent across all windows.
5. Being able to click on categories in the trade and stock screens is nice, but the fact that you have to click on a category first and then use the search filter is a bit annoying, especially on the trade screen. This is because objects can be loose or stored; they can be stored in bins, chests, cabinets, barrels, and pots... it's not easy to see the contents of bins on the trade screen, so you end up not being able to tell your trade goods from your pre-finished goods, and your 'blank' crafts end up getting carted to the trade depot instead of your decorated ones... rather a nuisance really. Being able to inspect the interiors of containers on the trade good selection screen, and being able to search for items which may be in a container before selecting the category would be extremely helpful.
6. This is something of a carry on from previous versions, but I can't think of anywhere it's possible to see active Guild/Temple demands and agreements. This is a problem because you can have dozens of religions in a fortress! When you agree to upgrade The Communion of Lepers or whatever to a Grand Temple, it's something you idly click on and then it's so easy to forget which of the 27 shrines you've got on the go you were supposed to fix, especially when you're already trying to remember other agreements you've committed to at the same time.
7. Can't remember if this is an ongoing issue, but battle reports for a creature usually refer to opponents in vague terms, such as "the marksdwarf". This can be problematic when twenty dwarfs dogpile a werebeast and you're trying to work out which one might have gotten bit. It's not the end of the world but this is unnecessarily vague, especially since in the graphical version you could even have a tooltip when you hover over "the marksdwarf" or whatever and it could expand on the information to include a name.
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Okay that's all I can think of for now, I guess I can always add more if something else pops up. Overall all though I'm really enjoying the new version.