Rose won the MVP because he was the best player on the team with the best record and they didn't see much of a reason to give it to Lebron at the time. Rose did not put up MVP numbers.
You could make the case for a few others as well, but the performance of their teams and their impact on that team was enough to offset that in the eyes of the voters.
Speaking purely from a statistical point of view [considering PER, EFF] Chris Paul, Tracy McGrady, D-Wade, Kobe, multiple big men, and a few others have dominated some years when they finished in the 5 for MVP voting, but the performance of their teams was not enough to warrant them receiving the trophy.
I think the record of the team weighs almost as much as the players stat line.

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