People need to remember that SM Naruto was not a match for Pain on his own. He had extensive intel gathered by Jiraiya/Kakashi/etc., three giant toad summons (one of which held his own against a weakened Biju), interventions from Fukasaku, Hinata, and Kurama, AND the fact that the most powerful Pain was out of commission until the others were taken out, AND the fact that Pain was trying to capture him alive. The gulf between their abilities is so massive it's actually ridiculous. Killer Bee is definitely stronger than Naruto was at the time, but that's not even close to being enough to defeat Pain--he loses every single time.