Certain mounts (like riding dogs) would not be able to wear certain types of armour. (Like fine steel full plate armour,which would crush the dog) Instead, each mount would have a limit for how heavy of an eq it can wear and what kind of eq it can wear depending on strength,size, and the type of mount. The armour would protect your mount more, making it better in combat than a non-equiped mount, and ensuring that your mount will not die as fast.
Although this would be an superb ability for all mounts, there would be downsides (sorry). Down sides would be that mounts would not be able to carry as much, and would loose much more endurance points when moving or carrying things. They would also be slightly slower slower in combat, and much slower with heavy armour (heavy armour compared to the mount's size.)
The third downside, which would NEED to be put in, is that mounts would need to buy armour like you buy feats. You would buy a certain armour from the (person) and the (person) would attach it to your mount. This would NEED to happen so players do not cheat by moving there mount to a desired area, than attaching eq(which would save your mount endurance). Instead, you would need to have a (person) attach it. (which would be in a town most likely) You would not be able to remove the armour your self, seeing how you are not trained to do that. (Reason: these eq would be very tighly put on a mount so it would not fall off while riding, and so mounts to do not try to remove it themselves

The (person) would be able to remove armour, but it would be costly (more money than you put it on for.)(Reason:this "person" is the only one who can remove it because he/she has special tools, and knows how to remove it from the mount without it going bereserk.)
You would also (yes, another downside) need to train feats that would allow it wear heavy,medium, or light armour without trouble.
So:the positive side is that mounts become protected and are better in combat.
The down side is that it heavy for them, and it is costly in many ways.
Although there are more downsides than positive sides (by a lot) these would all need to be put in so these mounts do not become all powerful. Otherwise, this is a nice idea (a long one also.)