I'm also curious to see why these colors are this way.
The reason is video signal generation. As you may know, the NES' PPU generates video directly in composite and does not, ever, use RGB internally.
I am not very knowledgeable about video signals myself, but the colour information is added onto luminosity information in order to be retrocompatible with old monochrome displays. The colour information is a high-frequency sine wave. The amplitude of the wave is the colour's saturation, and the phase of the wave is the colour's hue. Thanks to this it was possible to broadcast TV on channels that were supposed to be black and white without changing any hardware. Whoever came with this idea is pure genius by the way, but that's another topic. (With todays' policy I'm sure they'd ask everyone to trash their old TVs and force everyone to update to colour, and change all their cables, etc...)
The NES generate colours with an ADC with really few possible output voltages : There is only like 5 possible voltages (not counting the synchronosation voltages).
The colours are generated with a johnson counter that will create a square wave, "high" for 6 cycles then "low" for 6 cycles and repeat, for a period of 12 cycles. The phase of the counter correspond to the hue, so those 12 cycles corresponds to the 12 hues available. Column "$x0" correspond to the "high" voltage level and column "$xd" to the low voltage level. All other colours are synthetized by switching between the "$x0" and the "$xd" voltage, at different phases.
This also explains why it's not possible to control saturation, and why colours $2d is identical to $00 and $3d identical to $10. $0d is "blacker than black" and should never, ever be used, if you use it the video signal is invalid and the results are unpredictable.
Sure the palette could have been better if there was 15 different hues (this would have implied either a higher frequency crystal), and if the "$xd" column wasn't accessible, with the same # of bits. Unfortunately, whoever at Nintendo designed the PPU didn't make this choice.
In theory, the brightness of all colours from $01 to $0c is absolutely the same, compensating for the traditional "blue is darker than yellow" feeling we have (due to our eyes containing less blue captors than green and red). The YIQ colourspace was designed especially to compensate this, again for backwards compatibility to B&W monitors. The same applies too to all the other 3 lines. If you have a feeling that $0c and $08 are darker it could be either :
1) The particular RBG palette you used is a little off
2) Your eyes have a relative quantity of light captors for R, G and B that is a little off compared to what the YIQ guys designed