I personally favor Seto Kaiba, but he isn't a protagonist, so I'll have to say Yugi/pharaoh. I didn't really care for GX or 5DS, and zexal is...oh god, zexal...
Jaden Yuki definitely, I liked the original series more than GX but Jaden's optimism and spirit just makes it so much more fun watching him duel while that old pharaoh dude is so serious and boring. :xd: