Evil Windu
The "Master Chief"
I definately get the feeling that the Jedi Order as a whole has serious issues when it comes to discerning between good and evil. Not just Anakin Skywalker or Count Dooku, the entire Order has a difficulty it defining what is good and what is evil, or better yet, they have a difficulty even discerning it.
Yoda admits himself that more and more Jedi are uncertain, young and old alike. Free spirits like Qui-Gon Jinn, and their philosophy of the Living Force might be to blame. It's sad that Lucas had to use the element of the Dark Side "clouds" a Jedi's ability to see evil and to eliminate the threat it brings.
I agree this charade Palpatine has constructed is completely paper thin. He has risen from a mere Senator of an unpopular, backwater planet to Supreme Chancellor, the most powerful individual in the Galaxy, within the course of ten very short years. The Jedi know this. They know that the Sith Order has resurfaced and they know that both Darth Maul and Count Dooku were part of it. They know there is a missing piece of the puzzle somewhere; to me it seems strikingly obvious.
However.
There are reasons to see the reality of the Jedis inability to recognize danger. First off, Palpatine isn't much of a threat. He's worked hand-in-hand with the Jedi, and apart from Yoda's look and Obi-Wan's comment, the man is clean. Darth Sidious, or whoever they believe him to be, is the one they are looking for. Plus the fact that he is so close to them, it would seem unlikely that not only a Sith Lord, but the Sith Master would ally himself with the Jedi, or appear to be.
Also, in all of Palpatine's movements he acts as though his hands are being forced. He acquires the clones because of the Senate and the Loyalty Committee forcing him. The Jedi go along, having to rescue their own and aware of Count Dooku's threat. In fact, without Palpatine they might do the same thing. So, in this way, Palpatine stays beneath the radar.
Why, dont they see the Jango Fett - Count Dooku connection? Well, first would be that they certainly don't think Count Dooku would do anything to support the public. They truly believe that he is completely against the Republic, which makes him their enemy. Seeing that he is now under Sith control, or a Sith Lord (perhaps in their eyes the master of Darth Maul, perhaps in their eyes Count Dooku's death with mark the end of the Sith which is why Palpatine and Vader take them by surprise), they believe the Separatist Movement is the greater evil. Palpatine's consolidation of unfettered power is small in comparison to the power of the Dark Side, little do they realize that both are on the same team.
Another reason the Jango Fett connection hasn't hit them as a shock is because bounty hunters don't really carry with them allegiance. Obviously Jango Fett has a reputation, and regardless of the Sifo-Dyas mystery, it's feasible that both the Jedi who commissioned the clone armies and Count Dooku could be indepedently contracting Jango.
Count Dooku becomes more and more the red herring, the obvious Sith Master throughout the story for the Jedi, I think the Order may just assume that he is or was the Sith Master. There is only two, and they are aware that one died during the Battle Of Naboo, rather then make the assumption that the then Sith Master was another individual altogether, they believe he is Count Dooku (who had access to the archives / and was more then likely aware of Master Sifo-Dyas' death). It makes logical sense, if they had no clue about Sidious. And why believe Count Dooku on Geonosis, about Sidious. Like Yoda said, he's part of the Dark Side, and he apparently doesn't have a history of telling the truth.
But the evidence is mounting against the Jedi's inherent inability to come to grips with reality. Here are some of the pieces of evidence the Jedi know, and just based on these alone it makes it pretty frustrating to see the tnire Order get wiped out, and they don't even see it coming.
1) They know the Sith have returned, and they are aware of the Sith forename "Darth."
2. They know the Sith Order's goal is ultimately to control the Galaxy.
3) They know that the Sith had a hand in the events on Naboo.
4) They know Palpatine obtained his position because of the events on Naboo.
5) They know that someone placed an order for a clone army years ago, this someone was allegedly Sifo-Dyas who couldn't have placed the order because he was dead. This tells him that someone was posing as an imposter.
6) They know that someone who has access to the Jedi archives erased Kamino from the maps.
7) They know that Count Dooku is now a Sith Lord, and I think it's fair to assume they know he was aware of Sifo-Dyas' indentity, death and had access to the archives.
8) They had heard that a Sith Lord named "Darth Tyranus" contacted Jang Fett to become the template for the clones.
9) They know that Jango Fett was under the employment of Count Dooku, someone who is known to be a Sith Lord.
The most significant factor is the conversation between Dooku and Obi-Wan. It can't be brushed aside due to Dooku's betrayal of the Order, Dooku is sincere in his request of Obi-Wan's services. We know that because he gives Obi-Wan sensitive information. The Jedi should know this because there is no reason for Dooku to tell Obi-Wan any of this, there would be no purpose. Obi-Wan is captured, there is no information or need for interrogation. Dooku approaches Obi-Wan, attempts to entice him and honestly wants the Jedi Knight to join him. Why would he lie? There would be no need for it. So he could free Obi-Wan and then have the Jedi escape?
The only reason Count Dooku would ask Obi-Wan is because he is being sincere, this should be the only reason apparent to the audience or to the Jedi or to any other objective viewer. So, this in and of itself, makes Yoda's skepticism of Dooku seem stupid and irrational. Yoda, being the figure-head and virtual brains of the Jedi, puts the idiocy of the Jedi in perspective.