Why not just make it like in Anime? or even Evolve it...
Lets sey, we Have 8 (or even more gyms) and give ppls some time like 2 months to gather 8 badges. And run off League (every 2 months) Cup. So xxx ppl will play Q rounds. Lets sey with 3 pokmns, Until we have last 16 players. Then we go to Full Tag teams. And New Champion will born

Over that with 8 badges ppl can challenge E4. And can Challenge Champion.
This offer two titles:
League Champion> one how beat other players
Pokemon Champion> one how beat E4 and Champion
And if som1 is lucky and have both titles, he will become Master.
Not to mention we can run other small turnaments with smaller prizes.
As a rewards, i think Moderators can make some special pokemons, or items. Like Shiny pokemons. More Master Balls. Evo Stones, Vitamins etc.
But First We need Rules like:
-No legend poks: cos every one will run with them, and we dont want it, we want more poks not less)
-Moves that lay too much RNG and are overpower are banned (few as point: Confuse ray, Minimize, Double Team and other Evasion Moves or at last make only 1 move per team) you may like it, or not. But spam Confuse ray all day, all night its not funny and every one will run with this, same goes for Evasion that gives amazing fights against each other, when both players spam Evasion isnt funny.