I like flying mounts... they add a great deal of immersion and customization, and would like to see them.
However, not just as WoW did it.
- Flying should be an extremely rare and sought after privilege. And that's just the skill to fly.
- Obtaining a mount - mechanical or organic - would involve some significant crafting or adventuring achievements to be able to obtain
- They cost money to operate, either in food or fuel, and you occasionally need to stop to do that
- Have some sort of "cooldown" debuff to prevent them from taking off right after landing... call it "Refueling" (Mechanical) or "Feeding Time" (Organic) or whatever