The reason for the cry doubling makes sense, the old Game Boy cartridges didn't have all that much space, so they probably had to do some substitution for cases where they wanted the cries to be similar, in order to save space.
I doubt they'd change the cries for generation 3 and onward Pokemon, as they probably used 16-bit samples for the Pokemon they introduced (FYI 16-bit in sound terms is top quality. 20, 24 and 32-bit samples do exist but they only needlessly create larger files).
Lots of anti 16 bit gamers in this thread :(
The samples used in the first two generations were most likely actually 8-bit samples between 8 and 16 KHz for their sample rate (the Game Boy/color was only an 8-bit system), newer games probably use 16-bit samples between 22.05 and 44.1 KHz
Looking forward to Pokemon X and Y. White FC: 0862-2660-4156 / 3DS FC: 2492-4470-1418 / White 2 FC: 4556-7836-2644