The problem with that is all the people who aren't attached to Pokemon because of design or something like that, will pick the strongest ones and have the best teams. And then you just get the floor wiped with your team because you snubbed your nose at the most powerful frontrunners in favor of Pokemon that aren't good competitively, thinking that they just weren't given the chance. In reality, competitive battlers are always looking for the strongest Pokemon, and what's the top used Pokemon aren't top used because other Pokemon aren't given the chance, they're top used because they're some of the best Pokemon out there. Not all Pokemon are created equal in competitive battling.
You choosing to use Pokemon you like is certainly fine, but I doubt it will have much effect on the metagame at all considering so many people will just use Pokemon that are strong and beat you. :/ Although I guess technically it would be more challenging for you, but only in the sense that you'd lose a ton to people that know the metagame more thoroughly.