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Pokemon has so much luck in it that honestly if you have two skilled teams fight eachother then having a 'perfect' team will not really matter all that much.
Is 31 defense IV's going to stop a critical hit super effective thunder punch on your gyarados? The only stat where IV's really do count is speed and that only really counts if you and your opponent lack a choice scarf and have the exact same EV spread, nature and base stat in speed.
Plus, you cant really say 'A skilled player with perfect pokemon will -always- beat out a player with average pokemon.' considering how much pokemon is based on prediction and both players are theoretically playing perfect sure IV's will matter then but its more likely that critical hits and misses will play a larger role in the outcome of the match.
