I am a new GM running sr4. The players are also new at this. I am using the sr4 missions to start off with. My problem is the mage of the group seemed to be easily taking out the opposition in these missions pretty easily using stun ball. Most of bad guys have a willpower score of 2-4. The mage is dealing a lot of stun to these people and knocking them out with repeated stun balls. Any advise?

Play up signature and the consequences of goingon a wild magical spree. Include some better magical defense, including counterspelling. I don't run missions however so I may not be the best to recommend balancing them.

Ambush's and drones. Those missions were designed to be scalable so just change the encounters so there tougher. This is also where edge comes into play. Grunts should use there edge for those times they get hit by what ever they can't defend against.

...embed a mage with the oppos who has a decent counterspelling skill. Even better, make him or her an initiate (grade 1 or 2) with Masking metamagic. If the PC mage has not initiated yet he will not be able to pierce the mask so he will have no idea another mage is involved (until of course the NPC casts a spell). There are a couple of Mentor spirits which also aid in Counterspelling (I think Mountain is one of them).

Having the NPC mage summon a spirit can also help, particularly one with the Confusion power. Nothing is worse for the offending PC mage than to have his buddies go wandering off dazed, drooling, and confused leaving him all alone.

Also, don't have all the NPCs in close proximity to each other, that way he may only be able to get a couple with a stunball. Tit for tat, have someone fire an airburst Neurostun, concussion, or Nausea Gas grenade at the team. The sammy's may still be standing but the mage could go down or at least have serious enough modifiers to mess with his spellcasting.

Combat drugs & using Edge to go first can also be very helpful to give the NPCs a jump on the runners as well.

I think every new GM when they start playing Shadowrun goes through a phase of "this mage player is too powerful." I'm not kidding - they really do. You learn to deal with it.

I don't run the Missions games so I don't know what specifics to suggest, but the odd drone or dwarf physical adept can mix things up a bit.

Check you're not making any of the common mistakes with magic (no offense - you'd be something like 103rd person here who'd missed the same thing).

1. The number of hits you get is capped by the force of the spell.
2. Drain cannot be healed by magic - no stun, no physical, no way, no how. You overcast or fail to resist drain, you pay the price.
3. Visibility modifiers apply to spell casting. A bit of fog, smoke or cover can wreak havoc.

Other than that - tactics, tactics, tactics. This is not D&D and the opposition does not blindly walk up to be killed. Play them like an intelligent security team or military unit. One of the big principles of Shadowrun is that it's easier to dish out punishment than it is to take it. That's why there's so much reliance on stealth, tactics and deceit - he who shoots first shoots last. A mage with Stunball might be dangerous, but so is a security guard with an SMG and a smartlink. Seriously!

And above all, remember that one of the fundamental things drummed into all security forces in basic training is this:

"GEEK THE MAGE FIRST!"

It's implied in Street Magic, and called out in the FAQ

http://www.shadowrunrpg.com/resources/faq.shtml

"MAGIC

Can Physical Drain be healed by magic?

No. Damage from Drain must be healed by regular mundane medical care and/or rest. "

Healing drain is like buying money. Trust us. You can't do it.

Stunball is a pretty powerful spell, but remember, every time the mage uses it, he risks stunning himself. for most mages, it should have a drain value of 3, which means he has to beat three dice with charisma and willpower, a test most mages out of the box can only rely on getting 2 for.

2 5s in the Drain Attributes should get 3 hits on average. And it is not always Willpower + Charisma, sometime it can be Willpower + Logic or Intuition.

Getting x hits on average on being able to count on x hits is a very different beast.

If you need three hits and you get 3 hits on average then half the time your taking drain.