Here’s a thought.
We have base attack bonus, yes? Which impacts how well you can physically attack something.
And that is opposed by armor class.
At the moment, spells are (usually) opposed by saves, and (for those who have it) Spell Resistance.
Caster level impacts getting through Spell Resistance.
But, most don’t have Spell Resistance.
And those who don’t want to get (for example) knocked down by a mundane with a sword will need to invest in Armor Class AND Discipline.
Step 1: make Spell Resistance something like AC; everyone has it, and gear can provide additions to it.
Step 2: primary casters (those whose spells go to level 6 or higher) get 1/1 for magical attack bonus, half casters get 0.75/1, and non-casters get 0.5/1. They can spend feats to boost their MAB, with pre-reqs. Their primary spellcasting stat impacts their MAB as well (for non-casters it defaults to int or cha, whichever is higher).
Step 3: spells that just deal damage no longer have saves, those that have crowd control effects would deal damage as well as those crowd control effects and the damage would trigger if they get through the SR, but the effect would not if their target makes the save.
Step 4: spellcraft is changed to only provide bonuses for hard ranks, not soft ranks.
Step 5: skill dumps are made mechanically (almost) impossible; folks can only save a maximum of 1 skill point when levelling.
Step 6: dispelling would be required to breach their spell resistance to have any impact. This gives mundanes a way to try to build to keep their buffs/wards.
Just an idea, but, something like this could definitely help address part of the issue.
Please note that I do not know if this idea is even possible with the NWN engine.