As technology allowed for the worlds and aliens of the prequels to become a reality, George Lucas explains that Yoda was originally intended to be a cgi creation in The Phantom Menace. While they were able to pull-off convincing characters, like Sebulba and Watto, it seems cgi Yoda would still have to wait. Once it was accomplished for Attack of the Clones, cgi Yoda was then edited back into The Phantom Menace.
(Source: Entertainment Weekly: Inside Movies)