Here's an idea, probably won't work BUT, what about the [FANCIFUL] token?
It's wiki description reads:
Makes every civilization know about the creature. The creature won't occur in regular material preference lists. The tag also adds some art value modifiers. Used for things like dragons and other legendary creatures. Conflicts with [COMMON_DOMESTIC]
The idea: can this be used to reduce the dwarf/ponies want for the many added materials like the many types of stone and ent wood and whatever. (Probably not good for ents since it conflicts with the [COMMON_DOMESTIC] token, unless you don't mind ponies no longer bringing them with them during immigration.) But still if this token keeps the materials from showing up on preference lists and you can find a way to still get to them perhaps this could prove useful?
Theoretically, they could still bring them by dint of being allowed to claim any [PET], but that would require wild roaming trees, which I'm resisting because it looks dumb as hell to see migrating trees, and the slow speed of trees would mean they slowly crawl across the map, blocking more interesting or dangerous creatures. Moving trees does remind me, though, I'd better look into the werewolf trigger mechanism to see if I can do zap-apple ents.
Additionally, [FANCIFUL] is for creatures, whereas the ent materials are defined on plants and merely co-opted by the ent creatures. I could lump all ent tree woods together in the Simplified fork, so that we have a single "apple tree wood" instead of red, green and golden apple wood.
Mostly, though, I intend to solve the wood variety problem by making the various dye plants more widely available(including underground) so that Traditional and Ornate players can make any dyed wood with a little work and patience, and for Simplified, conjured woods are being genericised to fungal, flower, grain, leaf, worm, fruit and berry, and I might lump all painted tree woods together as well. The new stones shouldn't be a problem, as they're going to made by using rock flower extract as a reagent to distil natural essences, so all 16 varieties will be available if any one kind is.
Idea for differentiation between the pony casts.
Use [phys_att_cap_perc] to give them a higher cap on their attributes or [phys_att_rates] to reduce their rust rates. (same can be done with mental stats naturally)
A different approach could be setting the pop_ratio much lower for pegasi and unicorns so that you have to make due with the lower numbers, that way you can only use them in key positions and losses weigh much heavier.
Slowing down rust rate for attributes does make sense. Another option is to give earth ponies slower skill rust generally, because unicorns tend towards more specialised crafts(We'll ignore a certain legendary weaver, dyer, clothesmaker, gem cutter, gem setter, miner, liar and persuader from the show) instead of the general farm-work earth ponies get stuck with that tends to have them learn a little of everything unless you're hugely organised. Keeping skills longer than pegasi or unicorns would be quite valuable. I'd have to work out how to apply that to the other species, too.
Ooh, here's a thought, earth ponies could have higher learn rates for the teacher skill. Cherilee is an earth pony, teaching fits in well with the general nurturing and growing skillset earth ponies have, and it makes them more valuable as military assets because of training.
Oh, one idea regarding armour: Since ponies in the show tend to wear a combined peytral/crupper, I might just take the liberty of adding that in as a flanchard. A fixed piece of armour protecting just the upper and lower bodies. I might make it less effective as an armour piece, but I think the fact that it'll use more materials and thus getting a single piece that's masterwork is more of a gamble would be enough to differentiate it from peytral and cruppers, where you can somewhat make do with mismatched masterwork/exceptional.