I think the Thunder line is fine because you typically go Thunder > Thundara as your normal nuke sequence and the Combo from Thundaga is pretty much solely intended as a gigantic focused damage spike when all your abilities are up. Burst seems to be specifically tailored to be used right after you Convert, too. I would personally like to see Thundara stun more often, it doesn't seem to stun at all but I have only been using it in combos. If the stun works often enough like the debuffs from the Blizzard spells it could have some more utility in battle.

The Fire line could probably use something added to it for utility but I see it designed as a fast paced "burn your MP" Combo line as each step in the combo reduces the recast time so you can continuously be casting. If battles end up becoming more against multiple enemies I could see this spell line becoming your staple nuke when a PLD is in the group and has solid hate on a horde of enemies.

I think CNJ is better designed in the nuke department because you have reasons to use the -ra spells outside of Combos, but having some abilties exist solely for combo use isn't a bad idea. This stuff is also implemented with the long-term in mind so we might not get the reasoning behind certain abilities until new content arrives.