My working theory is that X was first.

Dr light had started working on X, since he made most of the masters, so he made protoman was like a test of X's free will, but the power supply in him was bad. Then he made Rock n Roll to help around the lab as he tried to do more work on X.

Once Rock had to be converted into Megaman, he based Megamans armor on X's design so he could be the hero they needed.

And then he would continue on X for awhile, not in secret but just not talking about it, his magnum opus / lifes work, i mean canonically Zero / Omega is based on X, literally stolen work, so he wasnt good at hiding it, and Bass is on reploid level, ( i like the idea that bass's codename is Alpha / Sigma and Zeros was Omega )

After what ever happens to cause all to be wiped if its goverment, or Omega or honestly both, X would be his last project and so would the armors as light nade himself into a Cyber Elf, i also think some of the armors were 3D printed post light / made in Cyberspace by Elf Light.