It doesn’t bother me that the Jedi are portrayed as a bureaucratic institution tied to the Republic’s government. It doesn’t bother me that they are portrayed as a centralized Order that has a unified philosophy. It doesn’t bother me that all Jedi are military leaders during the Clone Wars. What bothers me is the fact that they are portrayed as an Order that encourages celibacy and abstinence, and forbids romantic relationships and marriage. Personally, I think that one of the biggest reasons of why people don’t really like the Prequel Jedi is because they forbid marriage. Most people are against forbidding such a thing, as everyone considers marriage and romantic love as something natural. Plus, the Original Trilogy itself never implied that the Jedi forbade such things.
The same can be applied to the “Jedi must begin training at a young age” thing. I mean… Okay, the Original Trilogy implies that the Jedi begin to be trained at a young age, but there is a difference between starting to train a Jedi at a young age and having him join the Order as soon as he is born. The fact that Yoda said Luke was “too old” to be trained does not imply that Luke should have started training as soon as he was born. You could find a middle ground and say that the Jedi are usually brought into the Order when they are 14 years old, or something. This way, Yoda’s statement would have made sense anyway, since Luke was 22 years old at the time.
If Lucas had retained the bureaucratic and centralized aspects of the Jedi Order without introducing the rules about marriage and training at a young age, and had found another reason to make Anakin fall to the Dark Side other than attachment, then I believe that no one would ever think of saying that the Jedi are bad. Plus, not introducing the Chosen One Prophecy and the Balance of the Force would have avoided a lot of confusion about how the Force really works, and would have made things like the return of the Sith after Episode VI to be perfectly acceptable.