The lack of Bass in Mega Man 9 certainly ticked quite a few people off. Where was he? How could a character of his caliber be completely absent?
According to developer commentary in the Arrange Album booklet, Bass was apparently undergoing "adjustments" during the events of MM9. Not only does this explain why he's absent, but also as to why he appears on Dr. Wily's monitor in the final moments of the game. So, presumably, Wily was working on Bass. Why? Who knows; it's up for speculation.
Many thanks to Vixy and marshmellowman for the find!