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Mewtwo and Charizard don't actually have two megaevolutions: The "Y" megaevolutions are actually Primal Reversions, only the "X" ones are megaevolutions proper.
Both Mega Charizard Y and Mega Mewto Y embrace the true nature of the pokemon, the former being a flying type and the later becoming more like its Mew parent, wich fits with the theme of Primal Reversion .
Meanwhile, the X mega evolutions showcase the human influence on these pokemon, mega evolution being about the bond between humans and pokemon. Charizard becomes the dragon type so many people always wished it was while Mewtwo becomes more of a fighting machine as it was originally designed to be by scientists.
