Well since they announced doing many new films, I'm finding myself more excited about the idea they will do some that are set in the PT timeline but not entirely about the main story we already know. Imagine if they bring Ewan McGregor back for an Obi Wan story, there might be enough footage right there to pad out Episode 2 enough that you could remove anything you didn't like and introduce whole new elements. Chances are it won't be that simple but who knows.
Your suggestion of portraying a jedi Dooku has made me think of a pre Episode 1 film. I have long wanted to find enough footage from other films to add into Episode 1 that could suggest Obi Wan had already been assigned an apprentice who was lost and grew up to be Maul after being corrupted by Dooku. I know the ages are all over the place for this idea, but it would add elements of Dooku's fall from the Jedi Order, add a second apprentice for Obi Wan, and develop Maul a little. I don't think there is anywhere near enough footage in the Clone Wars to show this, but I think something like this could be shown with Ventress.
As for which canon to follow, I usually go with the idea that if its good then maybe use it, if it isn't good replace it with anything better.
Frankly I love the idea of a film with Dooku starting as a Jedi and ending up as a rogue Jedi. I also like the idea of this latest Obi Wan and Maul storyline making an Obi Wan centred film. I would like to say your idea of an Ahsoka film would round it all off perfecty, but the hardest thing is not knowing where she is headed in the series. I was toying with the idea of using the clip of the old Ahsoka speaking to her younger self, and trying to show her run away from her life with the jedi, only to later reappear as an adult and use the footage from the Force Unleashed showing Shaak Ti to portray Ahsoka, but I just don't think it can work.