I do think something has to be done to make all-cavalry armies less attractive.

One idea would be having cavalry units reduce growth due to horsefeed, but that would either be too minor or too crippling.

Making mounts expensive to maintain might be the best solution, alongside marksman traits giving anti-cav, and maybe spear units a square option to do extra damage vs cavalry that scales with how much the cavalry moves in a turn?

Also I'd have mounts give a penalty to accuracy with ranged weapons.  One faction gets to ignore this penalty as a trait.

Spider mounts exist, i got once spider from quest and once from recruiting a high level hero. There are also heroes with drake mounts i think.

building crystal mines and researching techs that improve crystal harvesting and unlock crystal equipment is a big investment.to start producing cavalry units you only need to research a cheap tech and find a horse resource then build a cheap "extractor" over the horse resource.after you upgraded your horse breeder you can start pumping out cavalry units for the rest of the game.crystal equipment costs labor too while horses don't.

Raising midly the upkeep cost of mounted troops sounds good. This cost could be in horses, that would effectively limit the total size of a player's cavalry (of course don't even dream of  applying this to the AI)

with only one upgraded horse breeder you can spam cavalry units for the rest of the game.horses are always useful and never become obsolete unlike basic crystal equipment that you get after researching the"charms" tech.if you want to rely on crystal based armies you need to research a bunch of techs then maximize crystal harvesting.those level 3 crystal mines(crystal trove) are quite expensive.my +80 production city needs 8 turns to finish a crystal trove. 

I always thought a system where instead of granting prone resistance mounts would be unequipped for the rest of combat if a unit was knocked prone would be interesting.

That would create a lot of counters to mounts, and it would be fun. You would be able to knock opponents off their mounts and continue fighting. It would also add some depth because it would penalize super heavy mounted units the most.

I see what you want to achieve with this, you want to avoid huge stocks of horses by changing the sources from unlimited to limited.

What about requiring stock buildings instead? Let's say that a city can keep only a small amount of horses, like 10 or 20, and if you want to stock more horses you need to construct a city building, like for example stables, that makes for additional 10-20 horses.

And yes, horses and wargs should have a small upkeep cost. They are not paid wages, but they have to eat and be maintained anyway.

Another solution would be to require a new horse each time a unit is "healed from death". I will explain with an example: You have a group of three mounted units, and one is killed in combat, leaving you with a group of two units. Over time the group is healed and one unit "resurrects" or more apropiately, it's replaced by a new soldier. This soldier has a new horse, and this horse should be substracted from the stock. And by the way, it should be the same with material and crystal.

I'd love to see higher quality mounts require movement up the tech tree in a unique direction.

Mounts do need to increase maintenance, and that maintenance increase should be based on the weight the horse is carrying.  Having a horse carrying platemail should require 10 times the mainteance of some half-naked dude with a spear.

What I'd really like to see done:

wargs changed to a food source

Horses become an upgradable resource, which you have to upgrade to various types of mount

Basic mount would be avaliable in shop.

Advanced mounts would require the necessary resource to build the unit, horses would be kept in the same pool to reduce micromanagement. 

You'd have travel horses, warhorses (can carry more) , coursers (+init, would repalce wargs), and saddle horses (+map movement)

MORE MOUNTS! Spiders! Drakes! Lions and tigers and bears! Oh my!

You'd have to research the appropiate tech and upgrade a horse resource to get access to an elite horse.  Upgrading a horse resource would also cost horses so you couldn't rush it without trading.

I'd love to see magical horses, maybe gained through quest, but that would require a tech being unlocked through completing a quest- and I'm not sure if that's capable via modding.

I'd suggest not making it separate resources due to micromanagement

The only thing about making horses globally harder to get is that, in combination with the Tireless March nerf, it's make the strategic mid-to-endgame much more tedious.  Strategic mobility makes things faster and funner.