There should be a reason to seperate nukes other than giving cnj/whm an ability to solo/DD,
basically, having nukes divided should be have a purpose behind it such as a factor influencing party play

for example:

a) using a modified skillchain/magic burst system, say a whm and blm both cast aero within 5 seconds of each other, this should conjure up a tornado at the mp cost of aero, this basically gives a reason to cross class certain spells and stop spamming if you need to rely on a party member

b) if whm cast aero, and blm cast fire within 5 seconds, the wind should give the fire an updraft and conjure up Ardor/firestorm, this would give a reason to stop spamming as you rely on party members.