Honestly, the most simplistic way to curb Augmentation in Awakened, and Emerged for the matter, is to put a hard cap on Initiation and Submersion, but only for those who have damaged their Essence. People who get shot right up, that Essence Hole will heal. People with metal in their heads and hearts? That should strip down their upper limits, even cause interference with resisting Drain and Fading.
Mechanically, Augmentation is just plain cheaper for short-term boosts. Considering the fact that, with enough Karma, Adepts and Magicians can get right back to where they were, and beyond, with no negative impact, and they can get more Karma by using those implants, Bio at least, and some Cyber, is almost a free power boost. In the short term, it's better. Long-term, it's better. It has very few drawbacks, especially in moderation - get a few Deltaware implants, not only do you have zero chance of Cyberpsychosis, but given the minimal ESS loss, two or three runs, at nearly twice the previous efficiency, put you on a whole new level.
Street Samurai vs Adepts, Sammies win. In a straight-up fight, they win. In terms of flexibility, they win. In the long term, with the constantly shifting tech, there will always be a new toy to plug in. They will achieve their goal first, and have a Luxury Lifestyle. They will survive longer, unless they go under the wrong knife. They don't attract the same attention.
Cyber and Bio creep me out, but mechanically, not using them can make you fall to the wayside.