The other day I was thinking about all the times in history where foreigners who were technologically more advanced interacted with another culture and how those instances turned out.

Colonists vs native americans
blackships vs feudal japan
etc...

usually it turns out bad for the lesser advanced society, either they conform or are conquered.

Ofc, this lead to "aliens vs earth" but that sci-fi route has been done before.

So I'm looking for manga with the same sort of theme, except instead of the 'invading' nation being technologically superior, I'd rather it be about magical superiority, perhaps magical vs non-magical.

Feed your head.

I haven't got this far, but I think this happens in Sugar Sugar Rune (which is better than it looks).

This interests me, but I can't think of anything much.

Elfen Lied, possibly, I guess, but not really. The general theme is how humans would react if a superior ('magical') race of humans came into existence (answer being 'kill it', of course).

I'd be interested in an example closer to what the OP intends, which is why I'm bumping with this shonky suggestion 🙂

The back-story told in the later volumes of Vampire Juujikai has that, magical superior vampires against humans.

edit: Witch Hunter could also be something you might be interested.