Andy's nightmarish experience with making the show was Patrick Stewart's evil plan!Am I the only one who finds it odd that Patrick quizzes him so much about whether he's a Star Trek fan, then just drops the issue and still helps him to make the show after he's found out that Andy isn't a fan in the slightest? He may have also been more perceptive than he appeared, and picked up completely on what Andy thought of his script, which he surely couldn't interpret as anything but insulting. It seems like very plausible behaviour for the character that PS is portrayed as to take it very personally, and because of it, deliberately put him through to the most idiotic TV guys he knows and possibly asked them to be extra annoying/unhelpful, all as part of his grand plan to slowly ruin Andy's life! He may have also put Andy's agent up to all the stupid things he does through Series 2, as his behaviour seems to be Flanderized somewhat from not very helpful but well-meaning to ridiculously idiotic, socially inept and with no thought behind it whatsoever!
The sitcom that Andy wrote originally just wasn't that funny/marketable.We never get to see what Andy's sitcom would have been like if no-one had interfered with it, and the only real assurance we get that the sitcom is funny is from Andy himself. At the end of the day, the BBC is a business and they needed to make a sitcom that people will actually want to watch. That's their (and Andy's) job.