There's another GIANT problem with going full 3d and, to an extent, even just flat 2d graphics. In the next release we're getting RANDOM creatures (specifically megabeasts, but the are still creatures)... now, there are ways around it, but in the end you need to be able to support the creation of new graphical bits for all of the new randomly generated things. Not to mention that Dwarf Fortress is VERY moddable, which means you would also need to support the creation of new graphical elements from the things people have modded in to make them fit with the rest of the game or you remove a very large portion of the moddability of the game. That's not to say that such things aren't possible, after all Spore has a creature creation system that can make practically anything you can imagine, or at least an approximation of it. However, that system took years to develop but multiple people working full time on it, and it doesn't do natural creatures well. That's one of the reasons they went 'cartoony'. At one point they had it so you could make very realistic animals, like a dog, but the way they moved was unnatural and so looked wrong. I haven't seen any actual fottage of it, but those are the words of one of the developers.
tldr: switching completely over to graphics would require a VERY (read many years of dedicated time) large amount of effort to support random and custom content.