Basically, it's for 2 reasons...
So they can make profit when you buy an extra system.
You can say this is Nintendo's way of having players be 'social'.
Basically, it's supposed to be all fun and games and meet people and trade with them and battle. You know, making a good image for the game/company. Also, it proves a challenge to complete your pokedex, and would be a bit too easy to collect all Pokemons if it didnt recquire any communications with other players.