With the release of Pokemon X & Y, I would like to say that X/Y are my favorite Pokemon games! They have significantly improved the quality that the franchise usually has achieved in the past few generations. Nintendo and GameFreak have really increased the amount of content and details to start...
My favorite Pokemon game of all time is Pokemon Yellow. It was my first Pokemon game, and it's also the reason why Pikachu was my very first Pokemon. Pokemon Black/White is a close second. :)