There's some hilarious discontinuity in the plot if I remember correctly.
Not really. The only thing they really changed about the whole show was three specific things.
One, Toapanga originally hated Cory when the show started. When they got together a few seasons in, they changed the story to Cory and Toapanga forever... and that they fell in love on the playground when they were like 4 or 5.
Two, Morgan, Cory and Eric's sister was played by two different actresses through the years. The show would make mention of this by saying something like 'Morgan, you look different' *look at the camera and kind of wink* and move on with the scene.
Three, Eric went from a mild mannered High School student to a borderline insane person through the years. Sane at the beginning, Eric was the comedic relief in the later seasons.
