It really is a terrible feeling when you pass over Japan on your way to Seoul... Especially when you have to sit in Seoul airport for hours and then fly back the direction you came from
But if it saves you enough money... well it seems like a good idea at the time!
Edit: And to the above poster, I'm not sure if you are serious or not but... They stop in Seoul because not everyone is getting off in Japan. That's the purpose of those flights; people are getting on another plane to somewhere else (and some are just stopping at Seoul).