The list is more a reflection of the politics of the time than anything else. If it had come out a couple of years earlier, Flair almost certainly would have been #1. But since he was in TNA at the time, they couldn't put him over to any real degree. On the flip side, Bret would have gotten the mid-20s consolation prize as someone who was too big a deal to ignore but still had to be punished for disloyalty. But since he was back in WWE's good graces at that point, he was right at the top.
As for Undertaker, I think his status in WWE can be chalked up mainly to two things. One, he's never been on the outs politically. Two, he's still technically active, so putting him over also puts over the modern product.