I was raised in the command line so the idea makes sense...if optional and stuff (AKA press ??? key to pop out input console).
What I'd enjoy, however, is expanding filtering as seen in the manager orders screen (where you can input "wo br" to reach "wooden barrel"). It has uses in almost every selection screen with multiple choices, like material assignment or wrestling.
Another option is replacing the +/-/↑/↓ confusion by using tab to jump between categories (and shift+tab to go back). This might not be optional but it is familiar. Anyone who used a GUI app (most stuff without custom widgets in Windows, GTK/QT/etc in Linux, and I am fairly sure that holds true in Mac systems as well) can adapt to that scheme.
I can see what the problem is though. The menus aren't integrated because they come from different stages of development. Some features probably where never given thought in the first place, and hence we get strange, placeholder menus with barely any connection to each other.
Each menu was coded separately and doesn't seem to have a common widget/input set. Their purpose is controlling or displaying one specific set of in-game data...which is great when debugging, but you need to cook the data, because it doesn't taste that well raw :P
So this makes rewriting the UI a nightmare at this point. It'll surely be a lot of quick code with repeated functionality and such, requiring to turn repeated code into functions, make widgets standard...then reform everything (IN A WAY THAT PLEASES MOST PLAYERS... imagine we get an awesome GUI but no quick keyboard input, or with different key combinations to reach an action...people will go INSANE) and polish it. It's no easy situation for Toady and I can see why he neglects that grunt work in favor of doing more delicious (and satisfying for him) new features.
Consider that when developing a game by oneself, there's only ONE big motivator...motivation! And motivation is usually linked to shiny new features, while bugfixing is a boring, tedious task. It's like cleaning up after partying hard.
By the way, I agree with Troodon. We have the "right" (notice quotes) to clone the game in our own view if we wish and we can. As I said ?? post ago, people shouldn't think creating the world is impossible (in gaming dev terms), it just requires motivation and time, and wanting to re-envision something is a good motivation, and Toady did the heavy work already in terms of design.
After all it's not such an unique or evil (I know what some of you are thinking so hold your guns for a while) thing to do. Many of your favorite games are possibly the author's twist on its favorite game. It's like because of Doom (and its popularity) we got Rise of The Triad, Duke Nukem, and eventually Modern Warfare/Bioshock/ETC. Inspiration != plagiarizing.