Elder Princess Shroob because of her 2nd form and the music for her form was very epic to listen to. Her 2nd form was also the most epic bosses I've ever seen. That's why I like her beside all the others. I just wish that she would come back in another Mario & Luigi game (if Alphadream decides to make another one despite the success of the four games) someday. I mean, who wants another Mario & Luigi game? I sure would love another one someday, if it takes probably another four or so years to make.
I chose Bowser because I found his battles the most fun. Not only as Rookie and Bowletta, but in his Partners in Time appearance he and Bowser Jr. made a great boss.