Well, it'd be fairly trivial to have most an earth pony civ, pegasus pony civ, and so on for a "divided Equestria" module, but no, I don't think mixing is going to be viable. There really is no way to change creatures on the fly like that, unless, for example, earth ponies have three identical castes per gender and somebody writes a program to rewrite the save raws and add pegasi and unicorns on the fly. That'd require either shutting down the game and making the changes, or the use of some kind of "Dwarf Fortress Script Extender" similar to the Elder Scrolls games. Merging civs just plain wouldn't work unless you have a whole bunch of entity definitions limited to spawning one civ and each having their own unique creature(copypasted with a new ID), and change the creature definition when they conquer another civ to represent the new balance, though it'd probably make more sense to wait for multi-racial forts in the main game. If somebody thinks there's demand for those sorts of add-ons and wants to write them, as always, you're welcome to go ahead and upload it, but considering the complexity already confuses some people, asking them to fiddle around in the save raws isn't something I'll implement in vanilla Pony Fortress. Calling a base mod "vanilla" feels weird.
Oh, and about gem ageing, I'd assume the way to do it would be to have some kind of reaction that takes a base gem and creates an aged version(maybe a few aged versions, to represent levels of ageing), but that leads into the problems of multiplying the numbers of gems available for nobles to demand. Maybe we could have a donation drive asking Toady for a [GEMCARN] tag. The whole "Dragons grow with wealth" thing is utterly out of our reach, though if the base game tracked a dragon's hoard, a script extender could, presumably, change the dragon's body size to match, but I can't actually program or have any great knowledge of the actual guts of Dwarf Fortress, so I'm just guessing.
Sorry I've gone a bit quiet, Terraria's new update has been keeping me busy.