Look at the basic striking ability of an average boxer compared to your local average local tkd guy. I think you'll find that generally the boxers are in better shape and more skilled at applying their art against a resisting opponent. I'm talking your average guy, there are outliers in tkd that will be able to defeat a boxer and vise versa but generally I don't believe this is the case.
Why? The boxers spend more time trainibg with resisting partners, conditioning and working skills that are necessary in a fight: stamina, head and body movement, reaction, the ability to take a hit. The tkd guys spend time on forms, one steps, board breaking, and other things that are less vital to producing a skilled fighter. Alive training with an unpredictable and resisting opponent is the key. It could be the same for any art. generally arts that train more alive be it a grappling or striking art produce better conditioned fighters on average. This is not to say the other arts like my tkd example don't, but I'm talking about your average school.
On average some systems are better. The individual is certainly a factor but the "individual not the style" cliche isn't so simple.