Great idea of replacing Yaddle with Shaak Ti in TPM, Vaderios. It could create some a nice bit of continuity between TPM and AOTC.

As for the same shot of the Jedi Council appearing in TPM and AOTC: I believe it's mentioned on the audio commentary of the AOTC DVD that the Council scene originally wasn't in the script, and that they decided to add it later. They created the scene using bluescreen footage of Ewan and Hayden, and pasting the scene together using templates and footage from TPM.