Cleese wrote for the two with a style so different that it's almost difficult to tell the same guy did it. That's because he understood comedy. Monty Python is widely considered the best sketch comedy troupe ever, and Fawlty Towers has often been called the best sit-com ever. That's why it has a huge international following among intelligent people, much like Python. But don't let your love of the first part of that combination blind you to the importance of the second.
Sharp characterization is the heart of the show.
You seem to be forgetting that many of the best episodes are not just funny, but also touching, sometimes very deeply moving. Those episodes worked because the characters were well developed and we cared deeply about them. And once the writers have MADE us care deeply about them, they are no longer free to mold them like putty. So when we see him behaving in ways that are violently out of character for the man, we feel abused. Lately, though, they've been dropping the ball far too often on characterization.