Smaller characters I would have liked to have seen appear...Owen and Beru. I'm surprised we never saw them. Would have liked to have gotten one with Anakin back on Tatooine (not counting the movie), along with Padme and Obi-Wan and delved more into that "should have stayed here and not gotten involved."
I thought we would get an Obi-Wan and Bail story at some point. Also thought it might be interesting to see Bail's wife as she was the woman who raised Leia.
What I would have loved to have seen for Rex is a post-Order 66 storyline where he stays loyal to the Republic. This leads to him being hunted down by Cody and setting up a confrontation between the two. It would have been an interesting switch to see Anakin's clone remain loyal to the Republic while Obi-Wan's (like the other clones) was loyal to the Empire.
I think SW can have a great future in animation, like what WB does with DC and like how Marvel used to do animated straight-to-DVD films.