The best defense against magic is magic. (Well, except for background count, but it's hard to arrange that in your favor.) Make sure you've got a magician (or even more than one) on your team with good Counterspelling to help against enemy spells and at least one good option for dealing with enemy spirits.
The best offense against magic is surprise and immediate neutralization. Take him off guard and bring him down before he can get off any spells at you, cast any spells on himself to buff himself up, or summon any spirits. If you really want him alive badly enought to risk your life, then hit him with Stick-n-Shock or Capsule rounds loaded with DMSO and Narcoject. If not, then hit him with the most powerful weapon you have with the most armor-penetrating ammo, and end him before he even knows there was a fight. If you can, try to be prepared, work out a battle plan with your team ahead of time, keep him from knowing you're coming, and in general try to have the fight on your terms, not his.
Recently in a game I'm playing in, we found that the difference between encountering a powerful mage when we weren't expecting it and encountering a powerful mage when we had overprepared and infiltrated his base to take him by surprise was the difference between having a long running fight in which our best combatant was knocked out before we finally barely bought the enemy down... and wiping out the enemy in a single initiative pass of all-out assault before he even got to act.
