From what I understand, the modifier for the 'damage boost' you get from the Thundara combo is highly dependent on INT. Almost to a point where if you increase it high enough, it's (almost) more potent than a critical hit Thundaga in a combo.
However, given the increased importance of Fire/Fira/Firaga/Flare in the new raids, I wouldn't jump on the 'INT for Thundara' bandwagon just yet. Increasing M.Atk is clearly better damage wise for those spells. Well, that and Elemental Potency, which from what I understand is equal to M.Atk but exclusive to just one element. However, it's still something to consider because the materias for Elemental Potency give a higher stat increase compared to that of M.Atk. Still can't quite decide which materia to put on my Feet slot.
Then again, given the fact that INT and M.Atk boosts from materia don't overlap in armor slots, you don't really have to worry about prioritizing which one to increase over the other. The one you should be worrying over, actually, is M.Acc, because mobs actually resist spells quite often now.