There are many options:
If you want to start from the real beginning you should take Red/Blue on the GameBoy;
If you want a long story you should buy Gold/Silver/Crystal ;
If you want a good story you should take B2/W2 (usally the sequels are considered better than the original B/W but you should check out B/W before because there are many references);
If you want a challenging Game you should pick either Emerald or one of the games from IV° gen (Diamond/Pearl/PLATINUM/Heart Gold/Soul Silver);
If you want to catch all of 720 of them and learn about Mega Evolution Pick the last entrys in the series as of X/Y and Omega Ruby/Alpha Saphire and after those play the previous games. The oldest the game is the less pokémon are in the game to catch but the game will be harder
