The problem is the inconsistent input system. The same task uses different shortcuts in each menu, which makes it hard to remember. Even selecting rectangular regions of the world is done in a particular way depending on what you are doing.
Inconsistency is awful for users.
I play the game for the fact that it is infinitely replayable. I play it so much that the menu is now ingrained into my very being. If the interface was to change, it would confuse me. It would take a lot of getting use to. It could work out better in the future, but right now, it at least works.
Everyone who plays it has different parts they like and dislike. Personally, I'd love it to have a nice API, so I didn't have to go through DFHack for every util I want to write. I'd pick that over a new UI.
Sure, it's inconsistent, but the inconsistency is consistent. I'll take that.
But that's really not the tradeoff. A more consistent interface takes less total time to write and maintain than one that has one-offs for every situation. Inconsistency makes future development slower.
And we only see the tip of the interface iceberg. I find it highly unlikely that the internal interfaces between components are any better. Everything about Dwarf Fortress gives the impression that their source code is probably a nightmare.
Which doesn't matter, of course, so long as it runs -- until you want new features and progress grinds down to a crawl.