Duel City arc is pretty much THE main YGO arc. For those that saw the anime there's the Noah arc and the DOMA arc as well, which kinda takes away that feeling (especially since Noah happens in the middle of battle city). Noah was fucking awesome, DOMA was very different in quality. At some points it was fucking stupid, other times it was fucking beautiful. In any case, the additonal filler arcs gives the anime a feeling there's no main arc. On the other hand in the manga there's the shadow games arc, duelist kingdom arc, battle city arc and memory world arc. Since Battle City is so long I'd say it could be called the main YGO arc, or something along those lines.
Also, dark Marik made battle city ten fucking times better.