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There are quite a few things I can think of, but what's most apparent to me is the gender differences. Audino is odd because it can be either male or female. Miltank and Kangaskhan are exclusively female.
Mantine was not introduced at the same time as it's pre-evolution, Mantyke. The pre-evolution of Mantine cannot breed, whereas Gyarados and Pelipper's pre-evolutions can.
I'm sure the last one is a mascot of a third version/sequel.(or I guess both for this case) while the other 2 are exclusives to the first set of games in a generation.