Honda is the best roomie, he seems like he would be neat (was beautification committee in the season zero anime!) and sensible so you don't have to worry, but he also knows how to be chill and have fun
I'm assuming things like Yami Bakura 'will trap your house guests in figurines' are outliers that should not be counted for the purposes of this question
Actually Anzu might be an even better roommate than Honda because she's so busy I bet she's rarely home anyway. You get to pay half rent with a fraction of the potential annoyance
in this scenario I imagine where she is like your roommate in America so she is out tirelessly pursuing that dance career and then she comes back to your shared place and immediately goes to sleep
Gotta make a case for Ryou. He's organized, and he can cook! Also keeps games in the house. only downside is his ever-growing Monster World board and Monster World accessories
controversial take: Kaiba is worst roommate. His decor is singular: BEWD. If you don't like BEWD he will shame you until you leave. all this is under the notion that he even needs a roommate but shhh
but best roommate...... I'm going to go with Yugi. He's low key.. he likes games, and he's respectful of others, but Tea/Anzu is right up there too. Maybe Serenity/Shizuka
Jack is probably one of the worst... spends all of his money on expensive things like unnecessarily fancy tea/cup noodles or his own action figures... probably not the best at cleaning up