Glad you came back to this, the portraits and animations look really good. I wish I could draw sprites like that, but unfortunately I have absolutely no talent for it.
Isn't the heavy armor restriction because of flight? The Rhea, being unable to fly anymore, wouldn't be the exception to this?
Some other things for advancement maybe is better agility(defense) on the ground from becoming accustomed to having to walk/run instead of fly, maybe becoming stronger or tougher than normal from all the unusual (for an avian) exercise its having to get, I would imagine avian communities wouldn't be built entirely with non-flying things in mind. Also, some mainline units advance to a sort of weapons expert unit with two or even all three of blade, pierce and impact attacks (drake thrasher, human halberder, knights), not having the ability to fly might free it up to carry additional or heavier weapons, or just learn to inflict different types of damage with its primary weapon.
The potion bomber idea is cool, seems like it would be a challenge to animate.