Since you used your user ID number to show your Dwarf Fortress cred, I will start by pointing to mine as a reply. Hey, go easy on me, it's not like I get to invoke it every day! But yes, I was actually the 30th person to register, back when Slaves to Armok was mostly a long list of features and a strange 3D thing with no connection to dwarves. And I do think that that is probably part of why I disagree with most of what you're saying -- ultimately I was attracted to the site by that gloriously insane-looking list of features for a Fantasy World Simulator; I loved the idea of Dwarf mode allowing me to play Dungeon Keeper in that world, but ultimately what I love most about it is the idea that it will one day have deep connections with that constantly-evolving fantasy universe, generated uniquely for my game.
But I'll grant you one thing -- you're correct, the 2D version was in many ways smoother, a bit easier to get into, and more balanced (it was actually more difficult of a game overall -- food was harder to get, the river was more dangerous, monsters could pour out of the chasm or the river or your well, etc.) The thing is that all of that came at a cost. The 2D version gave a more consistent, balanced experience because it always placed you (more or less) in the same situation, with very little variation. The additional challenges came from relying on game logic (limitless enemies pouring out of wells, the river, or the chasm) without regard for trying to simulate a world in-depth. In other words -- 2D DF was a game that you might enjoy a lot when you play it, but I don't think it's a game that had the depth (so to speak) that it has now. Every fortress was ultimately the same; every story was ultimately similar.
Going to 3D was always necessary in order to represent the kind of deep, complicated connection with the larger world that DF was intended for. 3D mode allowed me to build a volcano fortress, spiraling around the column of magma at its center to open up into a deep sunlit sea far below; it's what let me build a fortress hanging from the ceiling of a vast underground cavern, with major dining-halls and living areas inside of giant stalagmites, connected by a spiderweb of retractable bridges I'd pull in when the cave-sparrow men flew up to attack. It let me build fortresses deep under the arctic ice, fortresses concealed beneath human villages, fortresses spread across either side of a mighty river I'd dammed, and so on. It lets me send out an adventurer to scout the area where I want my fortress to start, then later build on the land they explored. All of this requires not just 3D construction, but complicated connections to the larger world that DF generated at the start. And (inevitably) it requires some trade-offs between making DF a good simulator and making it a good game -- it needs to succeed at both (that's why many of the changes to the way caverns and demons work were added, for instance, restoring parts of the guaranteed 2D progression for the 3D setting). If you just give up on the simulation aspect and say "well, a tightly-scripted 2D setting that is always the same makes for a more balanced game", you're missing part of what makes DF so unique.
As far as the interface and display goes... I'm gonna lean on my user number of 30 again, because I remember what happened when display was prioritized. I mean, Armok 1 didn't have the greatest interface, either, definitely; but a huge amount of work was put into making it look good. The result of all that work? Toady burned out on it, found it no longer interested him (because his time was spent on graphical issues that weren't really what had attracted him to the project), and eventually it stopped. DF was envisioned, right from the start, as a reaction against that -- as a game that would put that giant insane list of features first and foremost, and everything else secondary. As someone who has seen the results of both approaches first-hand, I think I can safely say that the game is better off when Toady focuses on what he finds most interesting about the project.
You might feel that the game is feature-complete enough for you and that Toady should stop and focus on polishing the stuff you like. (Going by what you're saying, I assume you felt that way all the way back in the 2D version.) But, well, he disagrees, and I think that it's clear that there's plenty of people who like the current direction that Dwarf Fortress -- at least, while it's not the only consideration, there are clearly lots of them willing to generously support it financially.
Obviously different people are going to want the game to go in different directions. But realistically, you're treating it as though there's a choice between "continue chasing the impossible dream of Dwarf Fortresses' list of feature-goals" vs. "sit down, be rational, and focus on polishing the game that we have right now like a sane person." The thing is, you are already eight years too late for that choice -- Toady already made it, much more starkly, back in 2006 when he decided to drop out of a PHD program to work on his dream game. Who are you to start demanding sanity now? He's already faced much bigger and more important choices than this, and (like the dwarves in his own game, when struck by a Strange Mood) has decided to work on what he wants to create rather than what people expect of him. He's fortunate enough that there's people willing to support him in that goal, but even if there weren't, I suspect he'd just find a way to dig a barrow in the ground and live on mushrooms while coding the game he wants to code.
Don't get me wrong, there's going to be polishing, and if the forum produces small and reasonable suggestions to improve the UI I'm sure he'll listen; I do think that, at some point, there will probably be a UI overhaul. But "put an extended freeze on features to focus on polish" is not happening; this here mine cart only goes in one direction. And ultimately? There's thousands of polished games out there. There's only one Dwarf Fortress.
(Also I am greedy and want the game to reach Wizard Tower mode in my lifetime!)
Finally, for what it's worth -- as far as I can recall I have never touched Dwarf Therapist in my life. I like the interface, warts and all; I find it strangely calming.