I think elemental defenses are done on an enemy-by-enemy basis or, at least, a family-by-family basis instead of straight "element alignment are its weaknesses/resistances". Bombs are fire-aligned but are weakest to Fire, Amaal'ja are weak to Ice (I believe they're fire-aligned, they resist Fire but not Wind). Most enemies seem to follow the elemental rules though, especially Elemental enemies.

I prefer the elemental system now where having the right elemental spell is great but if you don't you can fall back on an element that will at least do normal damage.