I remember being really confused by all the animosity towards JFA... and then I actually replayed it.
While I still think the plot and characters get ragged on too much, the general flow of the writing and script throughout the first three cases is very lacklustre. In particular, there was one point where a string of basic grammar errors almost completely ruined my immersion with the story.
The massive, massive leap in quality that is 2-4 truly astounds me.