This is a complicated question so please try and understand
I want to catch and use Pokemon at the start of the game(eg.wurmple) but I don't want them to be my league Pokemon
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It's not even a question. WHAT ARE YOU ASKING? WHAT POKEMON TO USE FOR THE POKEMON LEAGUE? You do know that you can store Pokemon in your PC, right? Well, catch Pokemon like Wurmple to help you throughout the game, then when you get to the E4, use some of the other Pokemon you stored in the PC. Then, store Wurmple (hopefully it's a Beautifly or Dustox by now...) in your PC. Just make sure that you use Rayquaza for the E4... Emerald is the only game (at this point) where you can catch Rayquaza before the E4, so take advantage of him while you can. He's still level 70, too. I think that's what you were asking. In other words, the Pokemon in your party aren't the only Pokemon you have!
You just switch Pok�mon as you progress in the game. You don't have to use them for the Pok�mon League.
If you want to get Pokemon for your league Pokemon then what you do is catch some in the start then when you get water fall go to victory road and happy hunting lv 40 Pokemon and raise them the level you want then go have fun kicking the elite fours behind.
Well then just use them in the first part of the game, and abandon them when you get to the league. Simple.
You can change the Pokemon you use for each battle by going to a Pokemon center and storeing Pokemon in the pc.
Here's what I would say to you:
You get your own starter, catch which Pokemon you like, train them in normal way, when you get to the Pokemon league or everywhere else, just leave your Pokemon in your PC, catch which you like for Pokemon league and train it until it reachs the level you want. Or catch any legendary pokemon.
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