I'd tend to look at what the magic is trying to achieve. If the objective is "hit target with large stone, thereby hurting them", that's a mundane effect brought about by magical means, and "dodge falling rock" would be quite a good ability to resist with.
If it's "terrify opponent with sound of thunder as rock whizzes past them", defending with Brave sounds good. "Initiate of Orlanth" would also work on the grounds of "thunder is my friend".
If the player hasn't bothered to work out some SFX for their magic, pick the highest possible skill to defend with :)
Then again, we have the classic tree-jumping contest to consider. Which would tend to suggest the opposite conclusion :(
Powered by hypermail