It would be interesting though, to point a genuine geology professor at DF and see what he thinks. The problem would be finding one with the patience to learn enough of the game to actually start digging.
Knowing geologists, they'd be more likely to get interested if you told them the game is about booze.
I'm a geologist, the booze angle would drag then in only if they were the ones getting the booze... I've a couple of geological gripes with DF but hey, it's a game.
I could make a few suggestions but I think some of them would damage gameplay (or at least not add as much as would justify the changes, but reasonable things that I would like to see include dykes of igneous rock, spaning Z-levels but maybe only as thick as a vein of ore but coming right from the bottom of the map to the top/near the top... Faults with fault gouge and where the rock has moved you should see a visible sign of the movement like off setting an ore body/other feature if it is cut by the fault...) and some would things might soak up too much processor time (either during world gen or the game itself... finite element arrays to handle flows though rock/soil layers... Allowing for rates and direction of flow/seepage to be found for any tile, based on pressure of the fluid and porosity/permeability of the rock/soil/free space).
Actually... How does toady handle flows at the moment? I remember something about water teleporting to the front of the flow? How is pressure/head calculated?
Reading about the new underground features I think things are about to get less geologicaly realistic and more underdarkish ... Which is probably better in many ways for a game...
Water pressure is purely hydrostatic- only gravitational potential energy. I believe porosity is zero, except for aquifers, which have effectively unlimited water generation/consumption potential, depending on how you dig into it.
I understand flows less well, but I believe there is somehow a flowing/not flowing state for water- if it's flowing, it check nearby for where it can flow to, and, to mimick hydrostatic pressure, it'll just include the entire body of water (or magma, if you pump it- otherwise, it is chunky and ignores pressure) for a lower connected place to flow to, as though it pushed the water there. I believe the lower the place is, the faster it will flow, but this is just speculating on what others said.
As for underground turning into underdark/lost world-type thing, this is indeed more fantastical, and meant to make the underground into more of a continuing threat like it was in 2d days, rather than being geologically realistic. The shots of the non-cave bits seem to indicate that the minerals themselves are generated the same way:plum-puddingish style. To me, having read about Anaconda copper mines, the veins are hilariously small. (And two-dimensional, which is a big flaw, I know.)
Though, I hear there are ways for bubbly caverns to form, if I remember a fantasy novel correctly (I pick up information in odd places)- if water is flowing through and rolls loose stone around, hollowing one out? I don't know if it's actual or not.
edit: There's a mod/project floating around somewhere that's aimed at finding and inputting the numbers on various materials(melting points, shear strength, etc) to fix them to fit reality where they don't already.