On the idea of making Augs look natural. Ring did ask Whisper why she didn't get a full dermal simulcrum with a proper skin texture which would almost make her look normal. She commented that she didn't because she wasn't normal. So obviously the technology to make augs look natural does exist but apparently the "off the shelf" models don't normally have it and its apparently very expensive. Beyond that, it appears that Augs are also a bit of a fashion accessory for some, who enjoy showing them off.
http://www.davidcsimon.com/crimsondark/ ... trip_id=98
As for sexual organs. Again, they might be available but expensive and Whisper may have avoided them for her own mental reasons (like she avoided the skin) or possibly they don't reproduce the sensations of sex very well. A lot of those organs are also responsible for creating and releasing the sexual hormones so the Libido might not be so high (Although admittedly, it would be easy enough to take hormone injections or have the augs designed to inject them into the remaining flesh requiring refilling once in a while).
Its hard to say on the idea of growing body parts back or rebuilding them. Christianity is obviously still present so maybe it had certain objections over the technology for some reason or another, or once Augs were invented, the development of body regrowth/rebuilding came to a stall. Heck, they were predicting that Electric cars would take over petrol based ones back in 1903, but it never eventuated because the oil was readily available and cheap so very little funds went into the research.
Heck, I seem to recall they've managed to successfully transplant an entire human arm from a dead man to a living one who was missing his. Imagine if they got a similar enough lower body of another woman who was a body donor and simply joined it to Whisper's. Even presuming that you couldn't completely attach the body to her living one, you'd simply have augs between her natural body and the foreign one. Transplanted lungs and other organs and she's good to go (Again, movements such as the "human purity" one may have made such technology illegal).