One thing that probably throws you off is just looking at the raw numbers. Yes, Johnson might have averaged a higher number of assists, but his assist percentage was less than Paul's. But the big thing is turnover percentage. There was a year in which Magic had TOV% (turnover percentage) of almost 25%. That is absolutely horrible. For his career, his TOV% was 19.4. Chris Paul is at 13.3 for his career. That's a rather large difference, and it's safe to say that this is why many of Magic's numbers are better than Paul's but Paul's PER is higher than Magic's.
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