If they both played 15 minutes, the difference between Shaquille O'Neal and Kendrick Perkins isn't that huge. Perk's big advantage over Shaq is that, when healthy, he can play more minutes. In 2008-2009, Perkins had to play 40+ minutes in four of the games of the Chicago series. I don't think Shaq can do that.
When Perk comes back, I'm expecting his level of play to be around what it was when he had a knee injury last season.