Prejudice is alive and well in the 6th world, play it up! Why wouldn't there be 'cyber-arm only' clubs around? Use the setting to your advantage and make the world come alive with descriptions, smells, sounds, hatreds, and bigotry.
Have to remember, people fear what is different than them, and what they fear, they soon hate

magic ability is still ultra rare (something like less than 2% of the population can use magic) and yet can do awesomely fanstastic things! This breeds hatred and fear in alot of people. So much so that I would expect people without visible ware to be getting alot of second looks and prejudice thrown at them all time. It need not be overly threatening... Maybe they have to wait an extra 5 mins for that soykaff, or the merchant wants 3 forms of ID instead of 2, or the police officer runs a triple check on their ID for a routine matter. If you trivialize the intangibles in the game you are not doing the game any justice (At least in my mind)
Just don't get too carried away

(it's supposed to be fun remember?) and be careful of trying to "tweak" the stats of things cause you never know, what you think is a 'great fix' to an issue could in fact cause you a major headache down the road (found this out through personal experience!!)
Magic is the long haul to immense power, but it takes time to get there (Karma cost), and usually ends up with people do overally relant on magic that they just can keep up in other aspects of the world (social interaction, matrix basics, let alone 'job' skills! ) the attitude generally becomes 'there's a spell for that' attitude. While there is spell creation rules, it's up to the GM to thoroughly review what a player is trying to do and ask himself "is this unbalancing for MY game? What exactly can the spell do, and NOT do?" if you put your magic users into "easy mode" they can rapidly unbalance a game!
Cyber/bio/gene ware allows for a huge boost in ability right up front, but caps out relativily quickly (essence is finite!). Judicious implantation of 'ware turns 'Mr. Average' into a God... At least compared to mere mortals. But once the body has been pushed to that edge of death (0 essence) there is no more to be done. The shallow will continue the hunt for that next greatest implant that will 'fix them up right'. The smart realize they have gone as far as they can physically, and begin to look for an other avenue of advancement (skills!). A cybered individual who has been around for a long time can usually do just about anything if he puts his mind to it (just maybe not very well, in relation to other things he can do) climb a wall? Sure. Take down a guard? You want him alive or dead? Smooze with high society? No problem? Infiltrate a facility? Ok. In short, they end up with a huge host of skills that (should) cover a broad range of topics and thus make him more adaptable to any and every situation.
The mechanics of a game are just bits of rules and dice held together by abstract words. It's the GM who creates the environment and turns the abstract words, dice, and rules into a living breathing world. It's the players who give the world flesh and strength. Be careful you don't break your world by introducing an imbalance... And don't let your players break your world by imbalancing it either!