I like the sound of it. 

Let me answer with my opinion on the issues :

1. I would say at first to be someone kind of coming of age quest. Our dragons to have some kind of quest to complete before they can be called "true dragons". 

2. Yes. A war between any humanoid species and dragons. 

3. I would say yes. Dragons were "known" to be masters of magic but only the old ones. Maybe our dragons could learn magic over the course of the RP. 

4. No. Dragons should be different in power. Let's say a fire dragon could be stronger in terms of physical strength than a water dragon while the water dragon would be faster and so on. Different castes should be a thing.

5. I would say both. Like the Germanic tribes. They had clans and they had full autonomy over their clan but when there was a threat or something that would affect all clans, the clan leaders would meet up. Also, a leader was chosen (usually through battle) of all the clans (also happened in Britania, Arthur's time). 

If you need help or something. I'm here ! I am not new even if this account is :)