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The only differnce is that the red version has 11 Pokemon which the blue hasn't. And the blue has 11 which the red hasn't.
They are as follows,Red-Primeape, Mankey, Growlithe, Arcanine, Scyther, Ekans, Arbok, Electabuzz, Oddish, Gloom and Vileplume.
Blue-Sandshrew, Sandslash, Meowth, Persian, Bellsprout, Weepinbell, Victreebel, Pinsir, Vulpix, Ninetales and Magmar.
So really the best version for anyone is if they like one lot of pokemon better than the other. ie.Like Vileplume better than Victreebel or like Pinsir better than Scyther etc.
On the whole they are both great games and lots of fun.