Here is an idea for a challenging boss, well actually 2 bosses.

One uses only physical moves and can also only be hurt by magical attacks.
The other uses only magical moves and likewise can only be hurt by physical attacks.

When one goes down the other goes into a berserk mode where it gets faster and or uses more potent attacks, so if you don't plan for that phase the boss will steamroll you.

I'll flesh it out a bit and send it to you later.