IMO the best solution is just having encounters that punish you for devoting too heavily to one side or the other. Not to say they are impossible, just much more difficult. It rewards the player for building a well rounded team without pushing specialized teams off the table. The easiest way to do that is to simply give certain enemies (where appropriate) percentage mitigation against specific damage types or simply magic/physical. I generally don't recommend immunities, but for very specific instances, such as single element immunity, it might also be okay.
