The reason their marriage was a bad idea, in my opinion, is that it doesn't really work with Guybrush' character to be married. He's a very, very boyish and childlike figure. Having him married feels wrong, and takes away from his character. Now, I'm all for character development, but marriage can't really be construed as character development, it's just a restriction.
This in addition to what others have said; where's the adventure when you know you need to go home to your wife eventually? Marriage is mundane, restrictive and has brought no laughs to the franchise.
It's currently ranking #1 on the Monkey Island Fail Scale, closely followed by the Monkey Robot.