I dispute the read on the 'it worked very well for a long time'. I think we are meant to understand the Phantom Menace as a glimpse at how the Republic and Jedi have historically operated. I do not think we are meant to read it as having only recently become the way it is.
This is Filoni's stance, and it's possible that he got this directly from Lucas.
I don't fully agree with that, I think there's a pretty persuasive argument that Qui-Gon's unorthodox stances and fixation on prophecy might have resulted in an Anakin who was messed up in entirely different ways, but I can see it.