There’s enough evidence for me that it was intentional, Lucas is fascinated by the fall of Rome and what happens to societies preceding their collapse. The prequels might not have communicated this idea clearly and it doesn’t mean everything was planned out, but the PT is in part about the dissolution of democracy and the fall of the Republic due to institutional failings from all sides that allowed it to happen.

Even in TPM the council was flawed, that’s why Qui Gon representing the wise old sage isn’t a member of the council and defies their wishes to do what he feels he must, typically out of compassion rather than self interest. Dooku fully defected from the Jedi but formerly trained Qui Gon, one deleted scene even goes as far to compare the two as respected intellectuals who went against the grain. Dooku became corrupted and was on the wrong side of the war, but shared similar ideals and both in fact did perceive a larger view of the force.

Palpatine in ROTS calls the Jedi dogmatic and narrow minded, then twists this idea to further confuse and exploit Anakin before convincing him and the public that the Jedi Order are corrupt, tyrannical and traitors to the Republic. That’s his entire manipulation game, secretly inciting incidents that would create the conditions to a more divisive political climate, then sowing seeds of doubt until any faith in the whole system is in question.

I don’t think it’s just typical bad guy talk either, maybe for us as the audience because the movies already let
us in on who the true good guys are. At the same time we point out where the Jedi Order were flawed we still understand they aren’t the problem, but if you were living in that society without the awareness you were being misled, maybe you would take the bait further and become a separatist like Dooku.