Well since the two shows are both aimed at kids it kinda speaks for itself that in those terms "Yu-Gi-Oh!" is a "better" show sience it displays the same moral standpoints as Pok�mon. The only deference is that Yu-Gi-Oh's main plot device is a strategic card game where no one is harmed while Pok�mon displays humans trapping lower intelligence beings into "Pok�balls" and letting them out to fight for their "Pok�mon trainers" pure amusement.
While some people could say that the trainer Ash could be a Japanese Michael Vick and that their Pokemon battles are cock-fights, Yu-Gi-Oh! uses realistic settings, weapons, and sometimes even "engineered humans" to battle before them. (I am using the TV show right now). Even though it seems like a simple card game, horrific monsters appear out of the simulation. Their violent fights are too realistic for an innocent child's eyes. Even though there is no blood or gore, the audience sees monsters that get impaled by their opponents. Yu-Gi-oh! encourages fighting with their cage-match type fights.
On a different word, Pokemon encourages friendship and teamwork. Unlike Yu-Gi-Oh!, when their Pokemon gets defeated, instead of exploding into terrifying shards, the Pokemon simply passes out and safely returns to the Pokeball.