With nuking, you have to know the target mob's strengths and weaknesses. For example,
Goblins are only weak to Light, and have no particular strengths, while
Crabs are weak to Ice and Lightning and strong to Water.
When you're facing an enemy that has no strengths to worry about (Goblins), and you don't have a spell that targets its weakness (Goblins), you can generally use your top two or three nukes regardless of element. When you're facing an enemy that does have strengths (Crabs), and you have spells that target its weaknesses (Crabs), you should avoid the spells they're strong against and concentrate on their weaknesses. You'll pretty much just have to learn these strengths and weaknesses, or keep some kind of reference handy and look at it for the two or three types of mobs any given party is fighting.
That doesn't mean just spam Blizzard and Thunder on Crabs, though. Fire and Aero can be effective as well, and if your party has a skillchain, you obviously should Magic Burst the appropriate spell. Really it comes down to MP efficiency and getting the most bang for your buck. Blizzard and Thunder may be more powerful than Fire and Aero overall, but they also take more MP. If you can do more damage with two Aeros than one Thunder, it makes more sense to go with two Aeros.
This is largely something you have to find through experimentation and paying attention. Personally, on the way up to 38, I found myself casting my 3rd and 4th most powerful nukes fairly often, MBing as strongly as I could, and Draining whenever it was up (most MP-efficient damage spell there is). I'd go with the most powerful two spells maybe once or twice per fight.