I never really understood why the force you to get badges to advance the plot of the bad guy team. I mean, Ghetis it makes some sense for, but most of the leader's final teams are only in the 50s or so, aren't they?
Why can't they just let you dick around and do what you want- you can keep getting badges and forget about the bad guys (Let someone else worry about that, right?) or focus on stopping them before you continue your champion career.
If you want to save the bad guys for post game, then so be it. (there Pokemon would simply be scaled up)