As some already said, it is because of the way they picked their teams. BJ tried to demoralize Pulver and simultaneously pick out the most ambitious fighters by calling out anyone who "wanted nothing to do with Team Pulver". Pulver mostly went for the guys who didn't buy into BJ's ploy, the ones who were there to be the toughest fighter they could be. So Penn ended up with a couple of good fighters and about five rockstars.
Penn is a great fighter but he is arrogant, which is why he is a great critic of his team but only a mediocre coach. Pulver clearly has more experience coaching (many years at MFS I guess) and is more humble and accepting, which goes a long way in coaching.