There are definitely improvements that could be made to the interface; the game allows you to micromanage labors but doing so for a large (the definition of such varying by player) number of units with the default interface is very tedious. Similarly, I feel there are a few other UI functions that could either be added wholesale, or improved. Who really uses the room display function, for example? Repurposing that into a tool for managing rooms, burrows and stockpiles all together would be nice (basically an "designated area" equivalent to the stocks menu).
I also feel that some of the interface problems are kind of tied into the game mechanics themselves. It might be possible to (as an example) have zones, burrows, and designations in general all fall under one general control, but doing so would require a rewrite to those mechanics rather than just how they're accessed through the UI. Likewise, while the take/feed stockpile system is a nice new mechanic for organization, the accessing that functionality felt more like it was just patched in to the existing UI, rather than trying to find a better, more accessible place for it. And then we have all those dfhack improvements that add, I feel, very useful functionality to existing menus (being able to search a text string in virtually any screen, and filter that screen to only the results, for example).
Maybe a lot of those will get done "eventually," although even I agree the UI is tolerably functional right now and bug quashing and new mechanics are more important than streamlining the interface, making it more user-friendly.