I agree with you, to a certain extent. Pepe seems the best, because we've only ever had the chance to see Pepe in action. Krasic has been off form, Elia too lazy, and the others are just not good enough to challenge Pepe as of yet.
However, should Pepe get some healthy and quality competition, we shall truly see what he is worth. I definitely don't believe that he's irreplaceable, nor do I hold him in such high regard as many others do.
He is invaluable to the setup, but I'm sure a quality upgrade with a footballing brain can most definitely do just as well, while making us look more potent going forward.