@anime_reference maybe Lost Magic? it was an RTS for the DS and shares with the games actually called Golden Sun being focused on elemental magic.
you cast magic by drawing a series of runes on the touch screen and you control groups of monsters you've captured RTS style (if somewhat simply iirc).
@alyssa I don't think this is it (looks too anime)
my theory is that I might've just imagined a DS port of command & conquer tiberian sun