\
Actually, if they were doing it more like the way pen-and-paper does it, your blast SHAPE would determine the save. Cone would be reflex. Aura would probably be Fort. Chain would be Will. Or something like that. Or they could make one of them give Spell Resistance.
A sizeable percentage of enemies are evil, yes. But it's also the most powerful blast type because of the synergy with ES, so I don't see a problem with it being mercilessly ineffective against large numbers of enemies. If it bothers you, make them like 75% resistant to it instead.
Make them stack Cha for DC's and switch up attack modes based on what they're fighting like EVERY OTHER CASTER IN THE GAME, and now there's an opportunity cost involved in the class. It's really all they need, you don't need to CHANGE anything about the class trees. Just make them INVEST in something so they don't have a ton of free feat and stat points to throw at whatever.