Maybe I should clarify this. The different tiers of thunder do not affect the thundercloud proc in any way. The only difference is, as you've said, Thunder II has 1 more tick, and Thunder III has 2 more ticks.
That aside, the way thundercloud procs works is, when you get a thundercloud proc, you can either consume the proc for an instant Thunder, Thunder II or Thunder III.
If you use a Thunder to consume the proc, your Thunder instantly does 240 potency of damage + applies a 18 second DoT on the target.
If you use a Thunder II to consume the proc, your Thunder II instantly does 295 potency of damage + applies a 21 second DoT on the target.
If you use a Thunder III to consume the proc, your Thunder III instantly does 340 potency of damage + applies a 24 second DoT on the target.
That's why thundercloud procs should only be used for Thunder IIIs.
The argument here is not really about what tier of Thunder to use for thundercloud procs, but rather which tier of thunder to hardcast during the regen phase.
For me, my theory is that Thunder has a shorter cast time and reduces the chances of clipping the DoT. The shorter cast time, which over the course of a fight, lowers the time you spend in regen phase and increases your uptime in the burst phase (which is the primary source of a BLM's total damage). Also, if you're thinking that by using Thunder, the DoT might drop off before you return back into UI3 to refresh it, its actually not an issue. If you're spending so much more time in AF3 (probably due to lucky streak of Firestarter procs), then it actually outweighs the downtime of Thunder, as a Fire in AF3 already does more damage than a whole cast of Thunder or even Thunder III that ticked for its full duration. This is due to fire spells doing extra 150% damage from 3 stacks of AF. (mentioned this in an earlier post)
However, some other people prefer to use Thunder II or III, for a myriad of reasons. There's nothing wrong with that, and you still will be able to do decent DPS, as long as the main idea of utilising procs and using F3/B3 to switch between AF3 and UI3 is there. I've seen some other lvl 50 BLMs still using Transpose to switch between states (true story), and that's when you'll be able to see a big difference in DPS as compared to other BLMs playing the optimal way.


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