I've been thinking for a while now about why it is I felt like there was a difference in the show right around the Waking the Dragons arc, and it's not just because it's a filler. I think coming off of Battle City, the anime wanted to get darker, and 4KIDS tried to keep it lighthearted, but they were delving into some dark comedy. On top of the seemingly endless reruns they'd do, it didn't feel "fun" as a kid, it was just depressing and a big bummer.
Even rewatching it as an adult, it was actually a bit of a hard sit because it dragged, for one thing, but it was dark and cruel to the characters (although Weevil deserved it, fuck Weevil). Yeah, Yu-Gi-Oh is a dark shounen at its roots, but while Yami Marik was a huge psycho, he was a fun psycho, cracking stupid jokes and just having fun. I think the Egyptian themes helped, too, and that got put on hold for the next two arcs before Millennium came in. Dartz was easy on the ears because of his voice-actor, but he's... kind of dull as a character. His subordinates were more interesting, but he weighed everything down with his alliance with Leviathan. The arc after that is so forgettable despite feeling like a safer rehash of Duelist Kingdom, I don't know why it even exists.
So yeah, Waking the Dragons fucked it up in tone and pacing, and it didn't really deliver, but 4KIDS had to make do with what they could, and bless their hearts, they tried.