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From what I've gathered, the blue routes are for Pokémon found in the wild grass and the red routes are for Pokémon found via alternate methods, IE. the honey trees, fishing or safari zone.
Given that my game seems to denote an Eevee from the mansion backyard to be rare there, I would believe that it denotes rarity, not means of catching. It was like this in Ruby, Sapphire and Emerald, so I don't believe it'd change here.
Wumple, Burmy and Combee are all common and Chansey and Hippopotas are pretty rare. Yet, the former have red routes, as they're all catchable through the honey trees, and the latter have blue routes, and they're both catchable the normal way.