YES. DO THIS. Or maybe, to preserve rarity .. you can ONLY have a golden/bronze/silver dragon if it's royal, BUT, royals can also be any other color. So that way if you see a gold dragon, you know it's a royal. But if you see a blue dragon, it could be a royal, or not.
2. Get rid of species specific companions entirely - make them all achievable by every one?
No. I like having SS companions.
3. Add more mythical companions in the future? On the flip side, don't add more companions it's confusing
No, don't add more. If you want other mythical companions, get a rougarou and have mythical forms! :D