It is pointless to talk about potency of a single DoT if you take into account only the amount of damage it does and you ignore its duration. A single Thunder does more damage than a single Aero II, but you can reapply Aero II 6 seconds before due to its less duration, so Aero II is definetely more efficient than Thunder. That being said, I usually turn to Cleric Stance and start nuking if the situation is under control. If it is a boss fight, I like to turn in Cleric Stance and then use this rotation: Aero II --> Aero --> Fluid Aura --> Stone II spam. The reason why I use Fluid Aura after Aero should be obvious: two spells in one single GCD. In particular fights like Demon Wall, I like to insert Presence of Mind in that rotation in order to maximazing the dps: Aero II --> Aero --> Presence of Mind --> Stone II spam --> Aero II --> Stone II --> Aero --> Fluid Aura and so on. I rarely use Thunder, because its MP cost is pretty inconvenient for a WHM.