Okay, here is some progress.
Water acts much better in some situations.
Most notably, water beneath other water will be forced to spread,
instead of having a random chance to.
This allows caves to flood much better.
Also, much more importantly:
There are cave ins!
They are very primitive right now,
but if you dig rooms too large, the top can fall in.
There are still some pretty ridiculous structures possible,
if you know how the system works,
and grand-scale things will hold together without issue,
but at least in most sensible situations, things will work nicely.
I haven't accounted for materials yet,
but at some point, stronger materials will be able to support more ridiculous circumstances.
I'll be uploading after I get these blasted trees growing.
Also, at the moment, I'm going to work on grass regrowth.
There is a very good possibility that grass will spread like fire to any appropriate locations.
I'm not sure I have a problem with it,
as if the effect is cool enough,
it should look pretty interesting.
EDIT:
I've solved the grass problem,
and now grass grows back gradually,
when there is adjacent grass.
I'm actually pretty pleased with the how it works.
Oh crap... I just thought of something.
I suppose if you got close to the bottom edge of the ground depth in the bluish stuff,
that the whole map would cave in around you very suddenly.
Well, I suppose I'd better add a few more layers,
then just hope nobody makes it that far until things are solved.