So a suggestion about display and challenge that I've thought over a bit.
That display idea I promised earlier
I had thought for a while that a good way to make the display easier to approach, especially with the new graphical tweaks, would be to draw not one layer at a time, but to draw the layer the player is looking at as well as every layer below it(to a certain point. Ten to fifteen layers should be sufficient.
Things such as unmined stone and open areas would be rendered as transparent, so that the next layer is visible below them. The exact render depth should be an Init value.
Every layer is rendered at 80-90% scale of the one above it, with the top layer rendered at 10%. Every layer is centered on the XY cordinate of the tile the player is looking at.
This allows a clear way to show the 3D aspects of the world as well as allowing players to see into those massive pits they've dug out, and in my opinion allows multilayer monitoring better than an isometric viewpoint would allow. I also anticipate that it would lead to more interesting fort design, such as balconies and overpasses, since such structures would now have a visual impact on what the player sees, and it has a minimal impact on the rendering pipeline, because ultimately, it's only an expansion on the viewport settings currently in place.(Render the current layer, the 10-15 layers below them, and have them stacked and scaled in the draw thread, which is almost entirely desynchronized from the game thread)
Another idea I had for this layout was the idea of making the opaque stuff on the current layer semitransparent, with a value in the Init files to let the player set how semitransparent it is. This allows the player to monitor stuff on both the current level and the level immediately below. I wouldn't advise more than one layer of X-ray vision of this sort, as it would get visually confusing, but in my opinion, the DFMA already shows the effect off nicely, so it's been shown that it can work.
An additional idea would be to have fluid layers --that is, magma and water-- be highly(or completely) transparent below the surface, so that a player can see to the bottom of a pool of water or magma at a glance. Perhaps making the surface layer of a fluid normal(or perhaps 30% transparent. It would be another Init value), while the underlying layers are all 90% transparent(another Init value) would produce a nice "haze" effect.
The idea here is to compress as much useful information into the screen as a player can make sense of, in a way that the player can make sense of it.
A couple of ideas for late-game challenge
Have Adamantine occur in nearly all tiles of the world, but restrict it to very deep underground, like under 2 or 3 layers of caverns, occasionally with a spire bubbling up like a magma pipe. This makes it a challenge to get to, particularly owing to the new cavern system being implemented, but also reduces the desperation of players such as myself looking forward to the endgame challenges which it brings with it.
Actually, I would like to see this treatment for both Adamantine and Magma. This would re-ignite one of the features of the 2D version, namely having Adamantine and Magma on nearly every map, while still making them challenging to get to unless you stumble upon a convenient pipe bubbling up through the strata. I believe this would also make for a more realistic representation, as in the real world, there is a layer of magma under the ground at all times, but it's usually too deep to reach. Digging deep is what Dwarves do best.
A special nod to semi/megabeasts
Megabeasts, to me, implies the creatures which are the world-creation legends. Dragons the size of mountain ranges, and other things like that. These are deities. Deities shouldn't die but once in a thousand eons. I propose toughening up Megabeasts to such levels, and after a certain point in worldgen, have them all look for deep caverns to go to sleep in. If you embark on a square with a Megabeast sleeping in it, the Megabeast replaces the magma or adamantine usually found in the hidden depths, and is orders of magnitude more frightening than any horde of demons if awoken, but you would usually find it sleeping as part of the terrain itself.(This could be represented as stone which is impossible to dig out, but would be better represented once creature sizes are properly added, with the megabeast waking up if you try to mess around with it too much.)
Semimegabeasts would take the place of current Megabeasts, but they too should have lifecycles. They should be allowed to reproduce only once every hundred or so years(with some variance, naturally), with fairly small litter sizes. They should be fairly reclusive and highly territorial, so that if there are too many of them, they will force each other into the open and get killed until there are few enough to hide in caves for a while, mate, have offspring, and begin the cycle again.