You seem to forget that high level skills still have high AP costs and high cooldown times.
If you have 1 'mega nuke', you can fire only one 'mega nuke'.
If you have 3 mega nukes, you can fire 3 'mega nukes'.
If for each 'mega nuke' you are allowed to have, even if they all take a whole turn to deploy, you are still allowed to fire an extra 'mega nuke' within a single encounter.
If one 'mega nuke' competes with one 'regular nuke', the 'mega nuke' will always win.
If a 'mega nuke' competes with a number of 'regular nukes' of a roughly equivalent total strength, that's actually a choice to make.
