I checked through the game's files, and not only did Roy and Mewtwo have the most development, but they weren't even the last characters to be developed, iirc, Sonic's, Wolf's, and Snake's files all came after Mewtwo's and Roy's. Also, while Sakurai hasn't talked much about these characters, he has allegedly stated that the roster (pre-Sonic) was finalized in 2005 and finished in 2006 (with Sonic being finished during the summer of 2007).

We also have official statements from him claiming that Dixie Kong was in the game, but eventually scrapped due to technical limitations, and I can't imagine that Dixie Kong was either the first, nor only character to be present on the files. I can't speak for all of the scrapped fighters, but Mewtwo's fate was less like Dixie's and more like Debug Mode's: Created and then discarded.