That's the point though. Modern tools might be more efficient, faster and safer, but the old tools work, and a skilled craftsman can do the job with the old tools. A skilled craftsman won't say he failed because his tools are older than 20 years, he might blame the complete lack of tools, but if he has any tools he won't blame the tools for failing.
If I have the skills, I won't need smart-gun implants, smart-gun gloves and shades will be good enough...hell, if I have the skills, I won't need smart-gun at all, only a gun. Better tools only improve my skills, they don't create nor substitute them. If I don't have the skills, then no amount or quality level of tools can get the job done.
You're still never going to be nowhere as good as someone with jacked up reflexes, smartgun and everything else will be. If you defeat an augmented character, it was not because of skill. It was because of smarts, using your enviroment, setting traps and just thinking a step ahead - and a massive amount of luck.
Sorry, now I made it seem impossible and it's really not. I mean, EMP grenade. I'm sure it'd be painful as hell for anyone augmented. But you're painting up skills too highly vs properly equipped. Take Robocop for example, the Cobra Gun - nuff said. Again with your example below, he uses his Mateba Revolver because he finds it trusty but it doesn't do jackshit against anything for the most part because it's too weak, but not only that he also lacks the skills.
Bottom line of what I am trying to say is, if you don't go augmented you can always get things that help still.
That being said, it'd be interesting to have a unaugmented character and it's a concept I've been pondering on myself the past few days.
Also, unaugmented tackle problems differently to augmented. If the heavy augmented NPC have their AI programmed to expect only augmented PC, then having non-augmented would throw them off.
The entire reason why Section 9 hired Takashi was because he was un-augmented. If the entire team were the same, they'd be predictable. And he only really started to get trouble with cyber crimes when he finally got himself a brainbox...and of course he still uses his trusted revolvers even though clip loaded pistols don't jam anymore as they used to and are much more accurate...
Actually the line she says is that she picked him because overspecialization leads to death - according to her.
Example; The cyberteam in Predator Concrete Jungle who ,while dangerous, are all vulnerable to EMP.
But if we actually look at it from a different point of view, the only thing he actually does is drive the car because he is for the most part incapable of handling anything else. Do note however, I speak from 1995 movie and not SAC, so I have no idea if he is portrayed better in that series than he is in the movie. But to my memory of the 8 episodes I have seen.. Not at all.