The Machete Order is only interested in what makes the best story. 'Fun having' isn't factored into it. And the original article says as much.
FAQ to the original article, which addresses many problems.
...That's it. Watching in chronological order makes it Anakin's story.The purpose of Machete Order was and always will be to refocus the story of the Original and Prequel Trilogies to be about Luke's journey.
There are so many problems with the production of Episode I, and Jar-Jar is simply emblematic of all of them. He isn't the most egregious flaw of Episode I, but he is the most obvious. Because he is the most obvious, that's what gets the most hate.