All these Pokemon games are geared to make you the hero.
What if I don't wanna be the hero? What if I want to be a bad guy, and join the local Team Rocket/Magma/Galaxy/Whatever? Or strike out on my own and be feared and loathed by all factions?
You can do that sort of thing in other RPGs, like Fallout 3. Why can't I have more options in Pokemon? Beating the Elite Four and becoming the Champion isn't always everything!
--
Proud member of the Global Defence Force.
http://gifninja.com/animatedgifs/120003/phoenixtrio.gif