The rule in question was written before they had those Runner's Companion qualities that could raise skills, so the omission may not be that significant. In several qualities, they specifically cite the augmented cap. In linguist, they don't. So either they only meant it to apply to certain qualities, and not others, or they meant it to apply as an overall rule, and only mentioned it for some of them due to sloppy writing/editing. Ultimately, the GM of this particular game will be the one deciding the issue.
On the overall character - Attributes and skills are not bad, it's just the adept powers that are a bit hyper-focused. I would consider replacing all of the improved abilities with, perhaps, improved reflexes: 1, agility boost: 1, and an improved sense. UmaroVI is right that tailored pheromones (and bioware in general) give enough of a boost to be worth the Magic loss. The only problem will be finding the resources to get them. But alphaware tailored pheromones: 3 and a synaptic booster: 1 (one example) will give you +3 to social skills, +1 Reaction, and +1 initiative pass. That's the same as kinesics: 3 and improved reflexes: 1, which would normally cost 3 power points.
