Simple issue is just the formulas involved, you can generate the problem mathematically after all.
Health formula is HD d X +(HD*Con). However, some creatures have significant HD above CR, and Con increases with level for all creatures except Con -.
Damage formula is CL d Y. CL is without shenanigans, generally equal to or less than CR. Additionally, Y is generally 6 or 8, while X varies from 6 to 12.
Area blasting spells do not differentiate significantly in damage formulas from point damage spells. They tend to have slightly larger dice, but thats about it.
So, for balance points:
-Single target blasting spells should have damage formulas comparable to creature health formulas, inclusive of rising hit dice values. Alternatively, have damage formulas comparable to archery damage at least.
-Blasting spells need a reduced random component. A large stack of d6s is visually impressive, but ineffective.
-Ability score to damage. Pretty much everyone but the rogue is dependent on this for a big chunk of damage already.
-Area damage spells should instead be geared after the health formulas of a CR-2 creature.
-Keep in mind that any changes would massively push the damage outputs of extant effective builds into orbit.
Single target, single shot - What you want here is to have your base CLd6+Stat, and then multiply it on higher level blasts, with more favorable multiplier:CL ratios on touch/close spells. More easily resisted/immune damage forms give you bigger dice, easier attack(touch attacks for example) or save half give you smaller.
A 3rd level single target spell could for example, hit for 2*CLd6 + 2*Stat. A 6th might hit for 3*CLd6+3*Stat. A Ray would go down to d4s, but a Fire Ray would go back to d6.
This hits hard, and punches through common resistances and health. It probably won't be oneshotting brute types, but anything else should go down quickly.
Multi targeting, multiple hits - Basically archery equivalent, so you base the formula off effective archery. Static base dice, stat to damage, CL gives more shots, higher level gives larger base.
AoE narrow(Line) - Approximately 3/4 of output of the point targeting spell. It'd hit likely 2 creatures at best. Width and length increases with level.
AoE wide(Cone, Burst) - Approximately 1/2 the output of the point targeting spell, but add a static amount to account for rising resistances(+10/20/30) for higher levels. Up the dimensions with level.
Damage over time - Difficult to balance, due to how fast combat can go. 2/3 of the appropriate category of damage(see above) per round is appropriate though, with fixed emplacement damage(like wall of fire) going to 3/4 instead.