It's important to remember that the credits, for many people, are the 'end' of the game. Therefore, you shouldn't put credits after the League if the rest of the plot isn't finished (and vice versa). What I'd recommend is making the completion of the League and the rest of the major events necessary for a final 'ending' section of the game-a final arc, basically. After that is over, run the credits.
This can be the final confrontation with the villain, a rival battle, gaining access to a Legendary (like Mewtwo in R/B) or Final Boss Trainer (Red in S/G), plot conclusion scene, or anything else you want. What's most important is that the credits don't roll until all major parts of the game are finished. Anything else, and you risk having players leave after the credits without finishing the other parts of the game.
Of course, it's fine to have things unlock after the game is over (Make sure you clue the player in somehow. This can be a post-credits cutscene or simple message appearing on screen.). It's also fine to leave side quests unfinished. Just don't let them miss the key components.