Picture Arceus with all of his plates revolving around him. You challenge him, he's Level 100, he has an aura which boosts all of his stats by 3 and suppresses all status moves you try to use on him, so no Topsy-Turvy or Toxic stall, and also suppresses all of your Pokémon's abilities in the same way Mold Breaker does. Now, everytime he uses Judgment, his plates start spinning and his type changes to something that's super effective against your current Mon (no Eelektross, hence Mold Breaker aura). You can't throw any balls at him, you have to beat him fair and square and I want this to be the single hardest battle in any Pokémon game ever. And when you do beat him, you don't catch him, he offers to join you instead, as he recognizes you as a worthy trainer. You can decline and challenge him again, but you also have to beat him again to get a chance to add him to your party.

That's my idea of how Arceus should be obtained, because the thought of catching the literal creator of the universe against his own will just seems so lame to me. Make something good out of it.