For me it depends on my mood. If I'm feeling energetic then docked mode is more comfortable and it's easier for me to stay focused sitting up. If I'm feeling tired then an easy game laying on the couch in handheld mode is better. I've tried tabletop mode before but the screen is just too small.
If forced to choose to play one or the other exclusively then I would choose docked mode.
If forced to choose to play one or the other exclusively then I would choose docked mode.