JBL had one good year as a main eventer and had a nice long title reign, but you have to look at the era he did it in. JBL was in the era of two world champions. I will almost guarantee you that if there were two brands back in the late 90's with two world titles that Shamrock would have gotten some sort of title run. JBL got his run on the B show and well it was decent there was nothing overly spectacular about it. He was a product of right place, right time. There were no other legitimate heels on Smackdown at the time and JBL benefited greatly.
You can't discredit JBL because of the era he was in. He still was a champion, and still has the longest reign in SD history. Before that he was a tag champion, then after that he had a solid US Title run.
We can speculate that Shamrock would have had some sort of a title in a 2 world champion WWE but he didn't. He was a consummate mid carder, while JBL although not at the top of the card after he lost the title, continued to stay extremely relevant.
Smackdown is the B show, but that B is very important, and being a World Champion on Smackdown means something. Just ask Taker, Edge, Hogan, Cena, Angle, Guerrero, Lesnar, HHH, Jericho, Hardy, Batista and others who all had the title on the "B" Show.