The modern interface is mostly intimidating, I think. Things aren't well explained and even the help menu is overwhelming in terms of all the stuff being thrown at you. There's 31 different menus accessible from the main screen alone, all of which have a number of submenus and have no indication of how important each one is other than guesswork.
Once you get used to it you can punch in hotkeys without really paying much attention, and still do everything you want to do with accuracy. It's helped by the fact that everything is available in two or three button presses.
In my opinion, for a game like Dwarf Fortress, where there is a myriad of things to manage and address, it is better to be able to navigate hundreds of menus in a small amount of time than to make everything friendly and organised. If it's possible to make things less intimidating while still maintaining the fast navigability (I'm not sure that it is, to any significant degree) then absolutely Toady should look in to it, but if it means sacrificing two or three key presses then it's not worth it.
The other things would be consistency and quality-of-life changes.
It's better now than, say, 0.40d, but there's still a lot of inconsistent hotkeys and layouts through the game. These are mostly just annoying to learn and I'm happy with the rate at which Toady is clearing it up. I might need to re-learn a key or two each update, but that's not too bothersome, and it makes things simpler for newcomers.
Quality of life changes, like the vein-automining, less crappy (but still pretty crappy) squad system, and the changes announced for whatever our next version is, are really cool to have in that they reduce the amount of key-tapping we have to do. And again, I'm happy to have these added one or two at a time as new versions come along. Adding a whole bunch at once would probably just result in me forgetting they exist and doing things the old way.
...
My WTF: I stopped playing DF for ~15 minutes to type this out. This game, it's a curse, I swear.