So BLM on FFXIV.

[Skies]

This is basically just an unfortunate result of how the two spells' combo bonuses work. Thundara's bonus is a ridiculous amount of added magic attack potency, which is why it does so much damage versus things like Ifrit. Thundaga's is contingent on it critting and even then it seems to work differently than Thundara (like a straight damage bonus or something). Personally, I think they should redo Thundaga's combo bonus into being something more reliable.

Now, who was it again... Kaeko? Yep, he did a lot of research on that sort of thing.
Essentially his work has shown that Thundaga in particular has +175 crit potency when comboed, and different from everything else in the entire game, it's critical damage is not capped by the 175% multiplier, it can go as high as it actually gets.