Well, the way my game is working is that I set the Basic Attack to deal both atk and mat damage (it's still a physical hit, but I don't know how to fix it so that it's both. I'm literally using def and mdf as purely for Physical/Magical Damage Rate, they're not even in any of the damage calculations (except that mdf is also my healing stat). I also have it set so that all magical abilities consume MP and all physical abilities consume TP (which has been changed through the aid of a plugin.
@SumRndmDde's TP Upgrade, if I have the guy's username right. Might be thinking of someone else, though (and if I am, I'm sorry for tagging you, haha XD)).
Anyway, the premise in my game is that mage classes have more MP and non-mages have more TP, their abilities consume some of either (or both), and that Attack is feasible for both archetypes. The damage of their skills are roughly equal because I'm using a dice-rolling system coupled with a lack of leveling.
Conversely, as I believe has been mentioned earlier, you could go DnD/Pathfinder-esque with your game and give the spells a certain amount of uses per encounter.