His reason for taking all pokemon wasn't to be the "best trainer due to lack of competition", it was to de-weaponize the world, making him and his servants the only ones capable of combat, and thereby stopping anyone from resisting them as they took over the world.
His original plan called for using N as a figure-head while he made the rules, setting up N as the invincible all power-full righteous charismatic King of the World, while he acted as the "king behind the king". When that fell through he went for broke and decided to rule the world through sheer power and terrorism.
Still, it's kinduva let down to go from someone wanting to be a GOD in diamond/pearl/platinum to someone wanting to be king, tho I gotta give it to him, he was a lot more crafty than the relatively straightforward Cyrus.
Still I think the best villain is me. Yeah, that's right, me. I have become the champion in Kanto, Johto, Hoenn, Sinnoh, and Unova; thereby establishing my dominance. I have captured a crap ton of legendary pokemon, granting me access to incredible power for future use. I have "freed" pokemon from the clutches of criminal organizations, keeping them for myself of course. Speaking of those criminal groups, I shut them down, simultaneously eliminating the competition and forcing the world powers to become dependant upon me for safety. I have raided ancient ruins for items and pokemon of power, making sure to tamper with or outright destroy the information there so no one else could use it. I have even seized control of the Distortion World and its ruler, securing an entire dimension to serve as my base of operations. The true scope of my plans is beyond the feeble imaginings of the so called main villains on that list, and has yet to be revealed.
But when the time has come, all shall bow before the one TRUE villain of the pokemon world: THE MAIN CHARACTER!!