Obito should have won during the fight but he was too careless and highly underestimated his opponent, maybe due to the fact that he's still young and naive.
He didn't use any of his arsenals at all besides Kamui.
If he had use Mokuton, Minato wouldn't even be able to get close to him since he could sprout sharp wood sticks in his body to pierce his opponents.
Minato's strongest offensive attack is rasengan, which is useless against Mokuton due to the fact that he has to get close to his opponent to land a hit.
All odds favor Obito yet he still lost due to the power of Plot no Jutsu, so that Minato could transfer the Kyubi to Naruto, which is the whole foundation of the manga.
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