Mages are really potent on a personal scale. That is very true. Offense is much better than defense, as well, and is in keeping with the overall theme of combat within the game. What often gets ignored, however, is their rarity. Granted, within a gaming group mages are often included, but in the world at large they remain very rare. There will always be more shooters than casters. Remember this, it will be mentioned later.
I have heard all sorts of people talking about invulnerable sammies or indestructible mages quite a bit over the years (the mage one is a little newer). I, personally, never noticed that problem. I have never noticed a problem with killing another person in Shadowrun. The opposite is often true: I find it hard to keep people alive. Right now, my group is low on the totem pole for shadowrunners, so they often run into the lower end threats. For the handful of tougher threats, they have kept their wits about them and dealt with them in an intelligent manner. I. E. striking first and striking hard, or sneaking around the problem, or even just walking away from it.
The balance, I've found, often comes from having tough, realistic opposition. Cover, as you know, provides protection in the form of LOS penalties. Toss in a smoke grenade, and only the guys with thermal vision will see through it. Also, recall that magic is a known quantity in Shadowrun. Technology has been produced to foul up mages, such as the smoke grenade that interferes with astral sight and thus interferes with spellcasting.
I think part of the problem you may be having is with a disconnect between what makes sense in the real world and what is a standard trope in fantasy or high fantasy. There are no evil overlords in Shadowrun. That is because anyone acting that stupidly dies. Seriously, the bit about the maniacal laugh? Dead. Kill the guy, you know he's a problem, so just kill the breeder. Why would you give anyone a chance to kill you in the real world? Sure, Shadowrun is a fictional setting, but that setting is the world as we know it, with just a new twist on it. People are still people. That stuff in the movies doesn't work in the real world and it doesn't work in Shadowrun for the same reason: it gets you killed. Would you give a guy a chance to kill you, the real you in the very real world? No way.
Bullets are cheap, and guns are in plentiful supply. As are random guys you can arm with said guns. There are literally thousands of regular security personnel for every single capable magician (1% of the world's population can use magic, but few of them become truly proficient). So, if some mage runs up, figuring he can just zap his way out of trouble, then the dozen or so sec guards blazing away at him will make short, short work of him. As for capturing someone, tranq or stun weapons are also plentiful, just knock them out and deal with them at your leisure, later. Why take the risk?
I haven't run into possession yet, although I have read up on it.. Parasitic FAB is a readily available technology. For those guys who are waaay too tough like that, FAB works wonders. Also, the hardened armor, while nice, is still affected by AP ratings, and you really only need to breach the armor with base damage + hits. AP ammo and a good sniper rifle, that takes care of most problems.