Jones beats Shamrock and Henderson because of his size and reach advantage. He would pick them apart from a distance and outpoint Shamrock and Griffin while submitting Dan in the later rounds. Wanderlei is a "pick-em" because of his raw aggressiveness vs Jones' skill.
Because of Jones' lack of knockout power, he has trouble with Chuck and Tito. I think he gets taken down over and over again by Tito with no real threat to keep him at bay leading to a decision loss and Chuck tags him a couple of times before knocking him out. I think Jones has been hurt and on wobbly legs in a few of his fights but his opponents were either afraid to attack or didn't realize he was hurt. Chuck knew when to pour it on. If he could, somehow avoid the bombs, though, he might outpoint him.
Finally, Couture is the worst matchup for him. His ability to wrestle and dirty box leave Jones no place to hide. He wouldn't have the power to keep him away, either. Power was the reason Chuck was able to come away with 2 out of 3 against Couture. He was either going to knock him out or get taken down. Jones just doesn't offer that threat and Couture would take advantage of that hole in his game.