If you were playing in an Arctic themed campaign, you might think it's a cool idea to play an ice wizard. Well, if you're fighting lots of ice creatures, that's actually a terrible choice. The folk of the frozen north should study and use fire magic. The desert nomads use ice magic.
So what do you do instead? In addition to making creatures immune to environmental effects of their home environment (letting magma beasts walk in lava unharmed), of course...
What I'd prefer, though, are special abilities and bonuses that trigger when you use the "wrong" energy type. Blasting the red dragon with fire hurts it, but it also lets the dragon use its breath weapon again. Using a cold attack on the frost knight gives him +5 AC for a round. Blasting a ghoul with necrotic energy gives it an action point.
I've nothing to add, really. Except that it could become fiddly to track the keywords of every single power the PC:s use against a monster. And that magma beasts do it half right. (They've got regular fire resistance, but get slowed if they take cold damage.)