I hadn't seen the timeline but I had guessed it was possible to figure one out (even if only roughly in some parts).

I've just been rewatching a few of the episodes from the first series. The episode Cloak of Darkness made me think maybe you could show Ahsoka being trained by several jedi, creating the implication this is standard, whereas Obi Wan tried to train Anakin all by himself and it failed (whereas Yoda was good enough to manage it with Obi Wan).

I also think this would be a good episode to use as, with a little cutting and reworking the script, it could give a cool introduction the Ventriss, showing her creeping around the ship without knowing exactly who she is before revealing her as someone who can take on a jedi master. I'm hoping they do a couple of episodes to bridge the gaps between this and a few of the following episodes so this story line could be cut down into a good half of a film introducing the three main bad guys. I may change my mind slightly depending on exactly what happens in the other episodes though once they are fresh in my mind again.

As for a story focussing on the clones. I've always been in two minds. Part of me likes them becoming more developed characters. However, I can't get past firstly, wanting them to be recruits from republic worlds rather than clones, and secondly, I can't help but feel it contradicts to have them originally shown as good skilled warriors, who we could even relate to and warm to, then to show them as stormtroopers who are fairly useless warriors, never seen as anything but fully helmetted symbols rather than characters.