KFK, you bring some interesting points to the field, but I think you under-estimate the advantages that Bay 12 has -because- it is only two men.
1) Bay12 doesn't have to deal with a publisher. This game is being developed iteratively, and is funded through donation. The reason the gaming world isn't littered with games with DF's depth is not because Toady is the first man to conceive of such a thing. He's just the first guy to come along and be willing to go all out, and get lucky enough to have a huge group of people notice and believe in what he was trying to accomplish. The world is littered with side projects that could have become something like DF, and did not. A major publisher would never go for a game that took this long to develop, multiple people can cut the time down, but attempting to at some point meet a deadline would vastly limit the scope of the project, and convincing your investors to back a project that has little to no -proven- mass market appeal won't cut it. DF doesn't count as proof of mass market appeal (to the people who make these decisions) because it has experienced exactly no market success.
2) The unity of vision present in DF is completely astounding. I think, in terms of complexity and man-hours spent on development, it is fair to compare DF to an MMO. You simply -do not- see this kind of coherent play experience in an MMO. You can very much observe the seams at which various things are stitched together, and MMOs suffer because of this. There is no infighting in Bay12 (or at least none observable), and Toady is a very un-compromising developer. A frequent complaint, and a valid one, is that the UI should be over-hauled, and Toady's "excuse" about the game being nowhere near feature complete is often over-looked... But it's not just a matter of the effort of re-designing the UI to include new features. The UI changes how players interact with the game, it is in and of itself a core game-play mechanic, and changing it -will- effect the development process. Console games are the most extreme example I can think of of UIs changing how a game is developed, but this applies to all games to a greater and lesser extent. Toady knows this is going to affect how things play out, and despite an enormous amount of pressure from the community, he is waiting to re-work it until he feels it is the right time. And DF will be the better game because of it.
When you involve additional people in a design project of any sort, you introduce a whole new bit of meta-design bologna. You have to deal with how people communicate, certain departments prioritize things around the considerations of other departments, and you lack a big picture. One man can try to lead a larger team, but you lose something in the transition. You can gain a great deal too, don't get me wrong... Toady would not have been able to make DF without Threetoe, for example.
3) Speaking back to the unity of vision, but on a slightly different note... This game is amazing solely because it is the realization of a dream. We are witnessing the birth of the game that is -the game- that most of us have wanted to play since we first sat down in front of our very first video game. Bay12 literally refuses to make anything less. And you will never find that level of dedication in a profit motivated organization.
I think DF lends itself exceptionally well to the strengths that Bay12 has, and vice-versa, and I don't believe that another game of this type will be seen for a great long while. I think that in order to develop a game with the depth of DF, the business model for game development would have to change pretty substantially, to allow for more of an iterative design backed by subscription fees sort of process. Because nobody is going to invest the man-hours to make a DF killer when it's only selling in one-shot packages for $60. It's not a financially sound plan.