I actually have put in quite a lot of time playing Minecraft, and the settlement system isn't the same... They are two totally different systems of creation, while serving similar purposes.... Only settlement building looks to be far more in depth than that found in most survival games that allow building... I mean, being able to have settlers living, working, and defending your settlements, as well as being able to set up brahmin caravans between them? That goes far and well beyond what minecraft entails. It's laughable in a way, to try to diminish the settlement system by equating it to Minecraft. Todd Howard mentioned Minecraft because it's the biggest and most well known crafting game. The difference in scope, and function between the two are easily seen by those who aren't against the system. The fact that it is also an optional part of the game as well..... Even if you don't plan to use the system, you've got to admit it opens a lot of great doors for people that enjoy those types of games, but also for those who wish to develop different character roles through roleplay.
As for them still working on the game, of course they are. They'll be working on this game for quite some time, even after it releases.