Is the element-related infrastructure of the game all mangled up, or is this it?

[Estellios]

I don't think the wands actually do anything to spells, they just determine what element your spirit dart is, so using a Fire-based wand would make your spirit dart Fire damage. I might be wrong, since I mostly stick to staves since I like their appearance and stats better, but it hasn't felt that way from the elemental stats on the staves.

As far as enemy element resistances, I think that a lot discrepancies have to do with way too much of the damage formula relying on your level vs. the target's level instead of any actual elemental relationships. If you fight stuff that's close to or under your rank, you do see major differences in damage between different elements, whereas fighting stuff even slightly too high your damage just tanks and any damage increases/decreases are a lot more difficult to notice.

That said I think the elemental system does seem to be working based on the triangles expressed in-game, and generally you can figure out what element an enemy is tied to based on the moves or spells it uses. Caster enemies you can definitely see a difference in damage between the different elements. I think you are correct about different enemies within the same family having differences in resistances, like elementals strictly following the elemental triangles and possibly the drakes having fire and thunder variants.