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There is no ultimate team. There are many great Pokemon available throughout Johto to use on your team. Likewise, the Elite Four and the Champion in the game aren't very difficult to defeat and should pose little challenge, provided your Pokemon are around the early 40s, at least.
But personally, great Pokemon to use include Gyarados, Ampharos, Rhydon, Espeon, Umbreon, Alakazam, Arcanine, Starmie, and Heracross, among many others.
That basically answers it - some pokes are better than others but there's no 'best' team, and most things will do fine if you train them enough anyway. Just in case, if you want advice on your team, post it in the In-game Team Help section.
Going to close then, nothing much else to add to this.