Well, Yu-Gi-Oh, is simply more intense. It's more hardcore than just dueling. They actually have (or, um HAD before 5D's) a plot deeper than some broad objective of CATCHIN' 'EM ALL.
I'm almost positive Yu-Gi-Oh is for an older audience.
“…Judge not what a man has done, but judge what he could have done if he was a different bloke altogether. For art thou a leper? And a leper can changeth his spots…” --Rudy Wade, Misfits (Series 4, Episode 8)