Of course the good guys and bad guys should never be as one-dimensional as you describe. Taking the OT as an example, Luke, Han and Leia are protagonist heroes who are undeniably flawed (though I’m sure you weren’t referring to them). At the points in the narrative where Darth Vader is pure evil and Obi-Wan is pure good, there’s still dimension and nuances to their characterizations. Vader and Obi-Wan aren’t just evil and good respectively, they’re a particular flavor of evil and good. They still have traits, goals, views, and rudimentary backstories. This is understandable, they’re not the protagonists. As the movies go on, they’re given more depth as we learn more. Vader actually has deeply repressed vulnerability underneath his cold hardened personality. Obi-Wan lied to Luke and either actually failed Anakin or is too hard on himself. Yoda and the Emperor are the embodiment of good and evil, but even still, have character traits.
I don’t have a problem with the characterization for Obi-Wan and Yoda in the Prequels either, I take issue with the idea that the Jedi’s beliefs are corrupt and incorrect and putting so much blame on the Jedi for their tragic fate. Protagonist Jedi characters should be good people with flaws, but the religion is the enlightened path, and the flaws of the characters (understandable and human) strays from Jedi philosophy (like Luke’s). The one PT Jedi flaw Lucas agrees with, the participation in the war, is a departure from their philosophy (though his intent is that they’re involuntarily drafted). There’s also still a place for characters like Yoda, who should be all good, because his purpose in the narrative is to be the wise mentor. You don’t see people begging for Gandalf to be given a massive amount of depth.
If a character is intended to be portrayed as a good person with flaws, then those flaws need to be properly shown, not overlooked. However, whenever you criticize Lucas’ portrayal of the Jedi in the Prequel Trilogy, it almost seems as though you expect every Jedi to be perfect. The problem is, if every Jedi is perfect, we are no longer talking about well-meaning individuals with flaws; we are talking about flawless people, which is an entirely different thing. For instance, hypocrisy can be considered a flaw, and if someone wanted to depict the Jedi as well-meaning but flawed individuals, it would be reasonable to portray some of the Jedi as hypocritical, at least when it comes to the Jedi Council. Yet, whenever someone suggests that the Council may have acted hypocritically, you tend to dismiss the idea outright, saying that you don’t like it. So, I believe you need to make a choice: either the Jedi are perfect, or they are not. If they are not, then their flaws must be recognized, and they need to have real consequences.
I understand that you don’t like the idea of portraying Anakin as a victim. However, the fact that he made his own choice does not mean that the Jedi didn’t play any role in his downfall. They were responsible for raising him and teaching him to control his emotions. And if they failed, it wasn’t solely because Anakin refused to listen, because there are many examples of individuals who come from challenging backgrounds and refused to listen at first, but who still managed to learn discipline and internalize good values. Yes, Anakin made his choice, and that cannot be denied, but portraying the Jedi Order as entirely blameless isn’t a realistic perspective either. Moreover, criticizing the Jedi Order is not an attack on their philosophy, but rather on the institution itself. The religion and its core principles are sound — no one is disputing that, not even many of those who criticize the Jedi. However, the institution, its rules, and its practices deserve to be examined and critiqued. This, again, has nothing to do with the core tenets of Jedi philosophy, such as controlling your emotions, living at peace with yourself, following the will of the Force and trying not to cause harm to anyone.
To give an example, the Expanded Universe often portrayed the Jedi as the good guys, while also highlighting their flaws. The EU authors were clear in their intent: while the fundamental beliefs of the Jedi religion were portrayed as correct, the institutionalized Jedi Order and some of the Jedi rules in place during the Prequel era were open to critique, like the ban on romantic relationships. In the old EU the authors were more inclined to make a distinction between healthy and unhealthy romantic relationships, suggesting that healthy romantic relationships were not impossible for a Jedi to maintain, while unhealthy ones — like Anakin and Padmé’s relationship — were wrong. This is an approach to the Jedi, their philosophy, and their rules that I agree with, as opposed to Lucas’ own interpretation.