I personally view Sigma as a character who worked to achieve evolution in order to overcome his own weaknesses.
Sigma was the proud commander of the Maverick Hunters. Built from the latest circuit designs, Sigma was arguably the most powerful and intelligent Reploid ever created. However, Sigma encountered Zero, who not only almost killed him but also humiliated him in the process. Sigma's pride was shattered; he was supposed to be the greatest, but now there was an entirely new level.
Sigma began to harbor a desire to reach that level. He wasn't the epitome of Reploid design; he could improve, he could be better. Reploids could be better. However, he didn't know how until Dr. Cain told him about X's potential. Sigma took Cain's words to heart and started his uprising in order to see that potential unleashed.
Over the course of series, Sigma made repeated attempts to obtain X's strength, becoming more and more obssessed. But no matter what he tried or how powerful his bodies became, he continued to be defeated. Sigma started to hate X for possessing the potential that he could never have. Driven by this hatred, Sigma conducted schemes to see X destroyed. The Earth Crisis is the result of that.
Then Axl appeared. A mysterious character who could copy the DNA data of any Reploid. Sigma saw a new opportunity; by obtaining the DNA of X, Sigma could finally find the key to the evolution he long sought, but he didn't count on Axl himself thwarting his plans.
After that, Sigma began to ponder what made X so powerful, eventually remembering X's dedication to justice. Sigma's views changed; realizing that evolution wasn't about power, he determined that he needed to change the world, correcting its imperfections and steering it to what he believed to be the natural course.
To that end, the New Generation Reploids were of prime importance. Because of their newfound viral immunity, they could not become Maverick from system abnormalities. They could only become Maverick if they wanted to be. Sigma embedded his DNA on the Copy Chips to share his mentality with the New Generation Reploids, to show them the flaws of the old world. By making them his children, Sigma made sure that the New Generation Reploids would carry on his legacy if he failed again.
With the revelation that a Reploid devoid of irregularities may still turn against the world, it was proven that Reploids aren't merely tools of the humans. That despite what some may believe, Reploids possess true, independent will. This put Reploids on a new level, forever changing the nature of human and Reploid existence. This is evolution, which is what Sigma always wanted.
At least, this is how I see it.