One way these issue can be balanced relatively easily is to increase requirements for the most powerful spells. And to decrease their damage initially - which would then increase as we invest more points into their specific governing attributes and skills.

So, at lower levels, you would not be able to simply invest one single point into an elemental school and get the very powerful spells of that school.

And if you can get some of the better spells early - they wont cause so much damage as they will once you level up and invest more points into specific skill.

While if you specialize in a single magic school - you will get appropriate higher levels in it more quickly and therefore you will be able to use more powerful spells of that specific kind and to their full potential.

I think this issue is arising from specific spells not being restricted properly then anything else.