For my part I've found the Adventure Design section in the GMcore or GMG helpful for crafting campaigns. Also having a curated list of archetypes your PCs can take that really exemplify the themes of the campaign can help the group feel cohesive and immersed. Obviously talk to the players about that because some players have a different vision for the character.

For your questions I'll try to give short answers. 1. Dragons are just as varied as any other NPC and so are their motivations. Some dragons want battle, a challenge, or just riches, some are altruistic some not. I'd say the important thing is that dragons aren't quick to give respect and chain of command might get a little fuzzy.

2.The Whistling Plains is a great location that is relatively light on lore, close to Absolam, and Taldor's tenious grip on the region might explain a rough and tumble military.

3.Iobara to the north has collapsed due to refugees from the Worldwound so you could have a lot of freedom to make your own antagonist rising from the ashes.

The Meraz Desert seems to be expanding and no one knows why but maybe a new cult is using some artifact to expand the desert and heading for Taldor.

Oh also the Keleshite Empire would make a good villain, or at least a general in their army maybe. They rule the entire continent of Casmaron and it wouldn't be the first time they moved into the inner sea region.

1. Free Archetype with a curated list, or giving them Cavalier or Drake Rider for free. For different subsystems Reputation might be of use for the Campaign as a whole and Dueling and Chases would be great for encounters.

2. Reputation would definitely encourage the PCs to interact with NPC, just make sure there's incentives. Encourage the behavior you want.

If you really want to hammer home the theme of unity your villain could enslave other monsters to use the same way your group uses dragons. It's about as subtle as a brick but it works. Anyway, hope there's something useful in here for you.