As said before, you should write the games' climax to fit with which part of the narrative is the strongest element.
While Black and White versions weave the two parts together, your League Challenge comes to a halt when the more important issue of stopping Team Plasma from fulfilling their goals. This is a much better way of writing a situation like this compared to the original plot of Red and Blue, or a more recent example in Platinum - where Cynthia literally walks up to the player after defeating Cyrus to tell them to get the rest of their Gym Badges with little fanfare.
If you're emphasising the goal of becoming Pokémon Champion, wrap up the major loose ends with other parts of the game before the player ends up at the Pokémon League. If you want to emphasise a fight against a team of antagonists, write the game as such the final confrontation is not revealed until the player has bested the League and built that up as the stories' climax - although it can be argued that a better standard of writing is to tie all parts of the games' story together instead of keeping them as separate plotlines that don't mix.