What people don't realize that Tobi was controlling the Kyuubi while he fought Minato and couldn't use his full strength against him. Minato is good against close-range fighters, because that's how his FTG works the best (eg. Tobi and A), but with long-range techniques you actually have the advantage. In this case Tobi has Mokuton and Fire release, and even if Minato dodged all of his attacks, his chakra gets drained quickly and then he's not even able to use FTG. Tobi instead has Hashirama's cells implanted into himself, so his chakra reserves would last longer.