Zharkaer 
Devoted Shimmerfag
Hmm, very interesting…
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Description
Note that having a red colour implies that it absorbs all but a low wavelength of energy - while having a green colour would imply that it absorbs all but a higher wavelength of energy. This could be significant.
Source
not provided yet
Comments
4 comments posted
Alphamon_Ouryuken 
Lord of the Empty Seat
Interesting theory…
Background Pony #93FA
It could just be a random animation thing and they decided, now that they have a higher budget a few years later, that red with purple lightning looked cooler and red was naturally the most evil color for the gems. However, theories are more fun. :3
ThePonyTheorist
Perhaps the green is an intermediate chemical? Before the red that makes up the magic?