One tiny, little, peculiar detail I just learned:
Batton Bones are prominent throughout "Challenger from the Future." These X-series mechaniloids completely replaced the Batton (Bubble Bat). Only a rare 30-year old Batton can be found in X1, Armored Armadillo's stage. This obscure Bandai-made game implies a time of co-existance for the two, right in the middle of the series interim.
Btw, I may write up an elaborate section on the Sigma Virus some time later.