I hate to go to this well again, but seriously, check out Joseph Campbell. In mythic terms, the Jedi absolutely needed to be destroyed in order for a newer, healthier, diverse system to take its place.
The hubris and arrogance demonstrated by Windu and explicitly stated by Yoda are evidence of this.
Qui-Gon sensed this, too, which is why he was marginalized. It'll be interesting to see how much of this is Incorporated into Obi-Wan's story. Being Disney though, I'm not confident they'll create something that serves the story more than something that serves their bottom line.