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Really it depends on the pokemon, and shinies are just for novelty value and don't really affect how you play the game, but still shinies are better because they're harder to come by.
Blue version, because it's localized and later versions don't have that annoying popping noise in lavender town that gives you headaches. Also blue is a more awesome color and Blastoise>Venosaur. Although Venustoise is clearly the best.