Cooper was omitted from the tournament squad, along with long-time captain Michael Hooper and another experienced flyhalf in Bernard Foley. The twice world champions exited in the pool stage for the first time.
Cooper had been in camp with the Wallabies all year up until the squad was announced, however, and said the level of preparation was in no way comparable to the detailed plans put in place by Jones's predecessor Dave Rennie, who was sacked in January.
"One of the things I struggled with in these last six months leading into the World Cup was we didn't really have a plan," he said in an interview with the Sydney Morning Herald.
"We had some great communication and talking around the game, but when you go into a game with no real plan or structure and no system, that makes it really difficult as a playmaker.
"Everybody is looking to each other. Are you going to do that? Am I in that ruck? It was quite tough."
Cooper said the selection of some of the assistant coaches defied common sense.
"Key individuals around Eddie lacked significant expertise," he added.
"As players, we tried to buy into what he was preaching, as not doing so would paint us as a detriment. However, common sense was hard to ignore, and it was remarkable that Rugby Australia couldn't see it.
"For instance, Jason Ryles, a rugby league prop, served as an attack coach for the Wallabies at a World Cup. How much did he truly know about rugby attack?"
Cooper said he had been upset at being left out of the World Cup squad and also bothered by Jones's later suggestion that he, Hooper and Foley were no longer the right role models for younger players.
"The thing that got me about that comment was more so that he questioned my want to win," the 79-cap playmaker added.
"My philosophy is to be the best I can be. It's about building good habits and foundations. That's a winning mindset...When people want to push the blame on others, that isn't a winning mindset."
Jones quit the Australia job less than a year into a five-year contract in October, having led the Wallabies to two wins in nine tests. This week he was re-appointed as coach of Japan.
"Coaches ask a lot of players," said Cooper. "I sat in on meetings and the coaches asked players to show loyalty for the country. It's quite a tough pill to swallow when you see some of the things that have transpired over the past few months.
"Players get one opportunity to play for Australia. I can't change allegiances tomorrow if I wanted to."
