For the DM:
One of the first rules about DMing should be 'know what you want to do'. When I say that I do not mean know what the players are supposed to do.
If you want a game that centers around action be prepared to 'create' that action.
For example:
A YGO game based off of action should 'not' mean that Kaiba/Jounouchi/Bakura challenges Yugi every other line. Make sure you have plenty of NPC duelists to challenge him with their own decks and styles. Make sure that you plan out for chances of physical action as well as well as break times where they can rest and regroup.
Don't yank history. If the game you are running is a Cannon based game then don't just change things at a drop of the hat to suit you.
For example:
You got a whole willing cast for your game which is a cannon that takes place after the Yugi vs Yami Yugi duel. But because of plot you kept Kaiba. Being a Puppyshipper AND DM does 'not' grant you the excuse of using the overly tired out Jounouchi's dad is a physically abusive guy to justify why the person who plays Jounouchi 'must' let Kaiba be with him. I seriously doubt any 1st world nation would allow a physically abusive man to keep a child regardless of age/sex/ or a sense of responsibility. The first responsibility of the court is the protection of the child. And you have no right to decide that the Jounouchi of your game was physically abused on your own. Discuss it with the player if they agree fine, if not don't just change history because you are the Almighty DM.
Also you created the villian but no matter how much you would like for it to happen. Not everything is going to go your way, not everyone is going to take the left door, not everyone is going to the Arcade instead of the Game Shop. No sorry, don't force them.
If you don't want a locked door opened and Yami Bakura has been enticed into opening it? Making him 'suddenly' lose his ability to pick locks is 'not' cool.
Yugi doesn't lose duels unless 'he' wants to lose duels. If there's no life or death situation or moral issue to make him stop the most a person can do is duel him to a draw.
(And yes I've been in games where all these situations came up.)
Being responsible is not a free ticket to being a jerk.
If you got someone who has taken Malik as a character but never plays him or even shows up. And someone else would like to take him? Its your responsibility to remove the player because they're not in use.
Just because you hate a character who has been picked for the game however. Does 'not' mean you can have them be the victim of everyone of your little malicious attacks.
Example:
If you don't like Anzu fine. But if she's active in the game making her the victim of every sick rapist in the city is 'Not' acceptable. Pointing out that she dresses in short skirts and shows stomach from time to time is 'not' an excuse.
Subplots.
When you start out you may not want any, so you can see what kind of players you got. But once you feel sure that you can trust them, and they want to make side plots. Give them something to chew on when the spotlight isn't on them. It gives them a chance to grow as an RPer and something to do that can contribute to the game later.