You're not missing anything. LEDs that have a high CRI is a relatively new market segment, so the selection is limited, and prices are high. LEDs use the same tricks as fluorescents to reach reasonable CRI levels-- multiple phosphors with different spectra excited by the lamp's primary EM emission. So the potential exists to equal or exceed the best fluorescents. Right now, the consumer LED market is focused on replacing lamps in non critical applications, and thus tend to be rather low color temperature and only modest CRI levels. This situation should improve in the future.
"High" CRI fluorescent tubes are available in color temperatures from 3000 to 6500K, with CRIs between 80 and 90, and at reasonable prices. Right now, this is probably still a good solution for many applications. If the performance of these lamps are not adequate, halogen lamps are the only reasonable alternative. LEDs are not quite there yet.
Not a complete answer, but here's some more info.
Brightness
While there are ways to calculate this that aren't that complicated, it requires knowing many coefficients that are not readily available, so ends up being an educated guess at best. You can do just as well totaling your current lighting's lumen output, then adjusting for changes in fixture styles. (I consider even a simple LED strip a "fixture" for the sake of this discussion) It's a starting point. If you use proper task lighting, there's a lot of room for variance in total levels.
Uneven light
You do not want to see the actual LED elements, it's really annoying. Besides diffusers, indirect lighting techniques work well, though require more lumens due to losses through reflection.
Positioning
I'm not sure what the issue is with parallel surfaces. The efficiency is mostly inherent in the fixture's ability to direct light where it's needed. The mounting surface has little to do with this, you need to direct the light where it's needed.
White Light
The "whiteness" is measured in degrees Kelvin. The temperature a black body must be heated to emit the same color of light. Standard daylight is often taken to be 6500K, anywhere in the 5000-7000 range is close enough for most tasks. You eyes adapt quickly to small variances. In residential settings, daylight is considered too harsh because we are so accustomed to incandescent lighting, so most home lighting is produced to output more in the 2000-3000K range to mimic the orange incandescent lighting.
Noise
How audible the noise is varies by manufacture and environment, as well as personal temperament. I don't think noise data is readily available. Testing in a noisy store will not yield any useful data, other than if you can hear it from a few feet away it is too loud. Noise can be attenuated by placing it in an enclosure, but keep in mind power supplies generate heat that has to be removed by ventilation, you cannot seal it into a sound proof box.
Try to place power supplies as far from your pillow as possible, trying to sleep is when it will be most bothersome. Placing it lower so there is likely to be more furnishings obstructing a direct path will help, as well as being surrounded by soft materials that do not reflect sound as well.
Best Answer
The first linked site appears to concern itself wholly with halogen bulbs. It claims of low-voltage halogen bulbs that, "They also produce a nicer light, with warmer, brighter and more vibrant colors."
The second site's entire argument for low-voltage light being better seems to rest entirely on how configurable and remote-controllable low-voltage lights are, as well as how much easier it is to scatter gobs of them about to achieve your lighting plans for world domination.
I am inclined not to trust the first site, because their argument doesn't make intuitive sense and they provide no citations to back it up. The second site's argument makes sense on its face.
I can't speak to halogen bulbs, but when it comes to LEDs, I would not expect any difference in light quality between a line-voltage and low-voltage LED.
I don't know of any LED bulbs that actually drive the LEDs at line voltage. The ones that you can just screw into a line voltage socket just include their own DC rectifier, the same way that CFL bulbs include their own ballast to drive the fluorescence.
I would expect you can get finer control by putting your own transformer in front of a line of low-voltage LEDs, and your resulting lighting system will probably be more efficient and flexible. (As an example, I know an LED retrofit lamp I recently installed could dim down to only 5%, whereas you might be able to dim the LEDs throughout their full range using your own transformer.)