Thunder is definetely in the rotation and you can use the procs to handle mechanics/

Here a great guide and a video that explain itselves :

Aikaal : http://forum.square-enix.com/ffxiv/t...A-Guide-to-DPS

Lavitz : https://www.youtube.com/watch?v=ZL8aIChlyQ8

Rotation in the vid

1. 6 secs before pull: Quelling Strikes > Sharp Cast > Ley Lines > Fire III > Enochian > Fire > Raging Strikes > Potion of
Intelligence > Fire IV > Fire IV > Fire IV > Firestarter > Swiftcast > Fire IV > Convert > Fire IV > Fire IV >
Blizzard III > Blizzard IV

2. Fire III > Fire IV > Fire IV > Fire > Fire IV > Fire IV > Blizzard III > Thunder > Blizzard IV

3. Fire III > Fire IV > Fire IV > Fire > Fire IV > Fire IV > Blizzard III > Thunder > Sharp Cast > Blizzard

4. Fire III > Enochian > Fire > As many Fire IVs you can cast until AF3 is low or you have to move > Firestarter > Finish with Fire IVs until you're out of MP then Blizzard III > Thunder > Blizzard IV