He offerred to spare the Jedi. He gave them a chance to surrender, in exchange for their lives. Neither Maul, Vader, nor especially Sidious would have ever done that for a couple of hostages.
And as for the yellow saber. It doesn't effect anything.
This is the second film in the series. Only Maul has been seen with a red saber, thus far.
There is nothing to support, in this alternate universe, that all Sith must have red sabers.
The "all Jedi use blue or green and all Sith use red" was destroyed the moment Mace Windu ignited his saber, anyway. What is he, a half Sith? Half blue, half red...
At that moment, saber color became cosmetic.
And to actually to compare what happened in EP II to the Vader scene in ESB, what happened in the original EP II was like:
Vader: Obi Wan never told you about your father.
Luke: He told me enough. he told me YOU killed him.
Vader: No. That's not true! That's impossible!
Obi-Wan's ghost appears.
Obi-Wan: No, it is true. Oh, and Leia... She's your sister, by the way.
The prequels seem to have this approach, that in turn is also altering the original trilogy to follow it, that every question is answered five minutes before it is raised and only the characters onscreen are out of the loop. Everything seems to be just going through the motions. The audience already knows the whole puzzle and how it is all going to end, not just in the larger sense, since we have seen Jedi, but in evry aspect of the films.
In the end of Clone War, the Jedi are still just as confused, but they are more divided. Yoda is sure that Dooku is the Sith Master. Mace Windu suspects that he is not and wants to keep an eye out for this "Sidious" and Obi-Wan is on the fence about it. Once again, just like with training Anakin, they are divided and incapable of making a decision. The arguement is more interesting in CW, because we don't know which one of them is right. It leaves the audience room to take sides.
And George's version is the one that is going to be redundant in the end, since the Jedi still don't know for sure that Dooku is a Sith in II, only we do. That means that he is going to have to reveal it all over again in Episode III for the Jedi, unless the Jedi are just left thinking they got the master, until Sidious is revealed. In that case, it works just as well that he was not a Sith...
Personally, I think it is more interesting to think that the Nute Gunray and Palpatine suckered in a Jedi by telling him the truth. The truth turns out to be so outrageous that no one will believe him, and the frustration of screaming the truth in a crowded room and going unheard drives him mad, and he ends out decimating his entire order, all in the name of destroying the Sith... And all the while, all Sidious has to do is sit back and watch. The Jedi do it all for him.
The Jedi's downfall in the end is no different from the Sith's a millenia prior.
They wipe themselves out with their own infighting and the Sith just have to sweep in and play clean up at the end.
I don't think that changes Palpatine's smile in Jedi one bit.
Whether he's thinking, "I can't believe another one is going to try this..." or "I can't believe he has the nerve to try this". Either way, whether from knowledge of the past, or visions of the future, he still thinks he knows how its going to end.