Not really. Game Freak balances the game for three different things I'd say:
- Single Player Progression
- Video Game Championships (high level competitive aka tournaments)
- GBU Singles (low level competitive aka laddering)
The game is pretty damn well-balanced in this regard. When you start creating your own custom rulesets, obviously it won't work out as well which is why all these convoluted bans and stuff are done by communities like Smogon and Pokemon Online. I think it's cool that Pokemon can be played in so many ways.