unless a show has 30 minute episodes, commercials aren't typically a problem if you want to see a full episode. most shows on CN seem to be using 11 minute episodes that are shown without commercials in the middle.
i always watch new episodes i want to see on CN because i want to see it as early as possible, and also because that's the only way that they can make revenue off the show. if i want to watch the show any other time i would probably do it online.