I've just posted this on bobgarcia's thread but it's important enough for general consideration.

A number of key scenes on Separatist ships and installations revolve around astrodroid lug-in points (the droid factory in AOTC, the hanger bay in ROTS) but I can't remember seeing a single droid of that kind on any of their ships.

In TPM there are the little droids seen walking around (presumably as workers) but they don't seem to have the necessary attachments.

In the OT R2 Units are pretty much everywhere, the Empire, the Rebels and the general population have them.

In the PT civilians and the Republic use them, so why would the Separatists be any different (The Feds have the same protocol droids as the other Republic members)?

Replacing some of the battledroids with more mundane droids would make sense in places where troops are not needed.