The prequel Jedi weren't that bad. They were complacent. Save for a few. Mace was pretty cool and even channeled the dark side in his saber skills.
There were so many Jedi, many who had not even laid eyes upon a Sith, that I could see the majority of them being naturally weak. They had bolstered their numbers sure, but a lot of them lacked focus and training on a personal level. The Sith had been patiently waiting, planning for their inevitable return for a very long time.
The prequel Jedi weren't a bunch of bumbling Jar Jar mascots. They were just not trained to the fullest extent. The majority, anyway. Personally, I think their portrayal was done adequately enough.
