Thanks for the thoughts, guys. Looks like this idea wasn't quite fleshed-out enough to post here yet.
Let me provide some clarification as guided by your questions:
The plan is for a 3D roguelike -- so instead of 2D tiles being the basic unit of space, we have 3D cubes. Each cube has a composition -- dirt, rock, water, etc. I am indeed looking for a "crafting system" which combines different terrain types to make new ones. The difficulty I have is that most terrain types are solid and thus don't really seem like they could combine with each other, and there's only so much you can do with magma and water as your two liquids. You get a bit more variety if you add temperature to the mix:
* Wet stone + freeze -> shatter, creating rubble (dirt?)
* Magma + freeze -> stone
* Magma + water -> steam (also water -> boil -> steam)
* Dirt + water -> bush (partial cover)
* Bush + water -> tree (full cover)
* Tree + steam -> jungle (impassable)
* Dirt + heat -> sand (reduced movement speed? Fluid? How would it interact with other terrains if so?)
* Rock + heat -> glowing hot rock (causes heat damage)
But can anyone think of a way to have two adjacent solid terrain types interact?
Should they interact?
My comment on movement abilities was mostly in that I don't want the player to easily be able to bug out of difficult situations. Stuff like teleporting large distances or instantly leaving the level entirely are pretty common in many roguelikes (including games like Diablo and Torchlight here, though they're far from the only offenders). This reduces tension. Movement abilities when used for positioning are fine, though they can be taken overboard -- for example, I think it's probably too easy in the Disgaea series to put your characters where you want them, much as I love the concept of tossing party members around the board. Mostly you just need to pay attention to how the movement abilities you've provided affect the tactical game and make certain they're useful without getting out of hand. So yeah, some limited movement abilities should probably make it in.
As for regeneration, I really, really don't want the player to be able to "rest" to recover. It's boring and and overplayed concept. The ideal I'm shooting for is that the tactical game never really stops except when the player finally does concede to attrition and flees the level. A skilled player should be able to steady-state by taking advantage of the instant-recovery items monsters drop, but otherwise you get those three restores which have to be rationed across the entire dive. Maybe there could be random one-shot fountains to give you a boost, but they shouldn't be able to be relied on.
Certainly once I have the basic mechanics in place, it should be straightforward to add more ways to take advantage of them. Monsters and traps that can manipulate the terrain are an obvious outgrowth of having an interesting terrain system (though tweaking them to be fun and interesting themselves will doubtless be an iterative process).
Thanks for the Terraria recommendation, baconman. I'll have to check it out.