I kind of just feel like "make an interface designed the way humans work" is just a buzzword sort of phrase people use without any sense of what they're actually trying to say or imply. For some reason people think touchscreen gestures are some how more intuitive than an interface that reads like a manual, a manual that's literally readable by anyone that can read English. The problem with DF's UI isn't the layout its the features that are accessed via the UI.
I don't see how something like (H) Hotkey, (i) Zones, (p) Stockpiles could get any clearer than it currently is in terms of actually interfacing with user input (you know, a user interface), the actual method of using the interface is as straight forward as it can possibly get for pretty much every menu. However there are a bunch of complexities with the actual systems that you're interacting with that aren't entirely clear. What IS a burrow? What's a zone?, Why are my cows blinking with a brown down arrow?, I built beds and put them in individual bedrooms so why are my dwarves complaining that they don't have bedrooms?
These aren't UI problems and I don't think you can just "fix" them by changing the UI layout. Dwarf Fortress is always going to be a game that you need to read the manual(wiki) to play. You're not going to use Photoshop, Excel, or Maya by fumbling around looking for "human readable UI" either. Once you breach a certain level of complexity you lose the ability to mask complexity (which is what intuitive UI does), it just becomes more beneficial for the user and the developer to have everything laid out plain and clear and to expect the user to read about stuff they don't understand.
The good news is that once you play for a bit you'll find out that Dwarf Fortress is actually a pretty easy game with a very direct, simple, and consistent design/interface.