I don't see Agito being shoved into the villain role honestly. While Agito is a character Takaya has clearly had some difficulty locking down how he wants to play him, he is not some simply comic villain.
The guy's established history is a life that's been hell mentored by a amoral scumbag. His "desire for power" arises from righteous fury at society for allowing such utter injustices to occur. That's opposite extreme of "I'm amoral and just out for myself" folks. I'm going to take charge and fix it is still extreme but on the other side of the ball park. The villain version of that end of the pool is "screw it, I'll just destroy it all." The worst we've seen him actually do is be a hard ass and make necessary sacrifices for the ultimate goal of defeating Chronos.
He also has not taked opportunities that would have been worthwhile if his agenda was as the people here advocating a Evil Agito claim. I still am wondering why he showed Balkus mercy and didn't finish him off.
Manga Sho has... largely just whined and stood by doing nothing while Evil Men did Evil Things. Thanks to that his body count of killed innocents utterly eclipses anything Agito has done.
-Died, but got better
-Killed his own father while not in possession of himself
-Had a few people who he knew a week or so die on him and in one case turn on him.
-Murdered a significant portion of the population of Tokyo to get at Khan. To my knowledge he has not acknowledged this atrocity.
-Saw his parents commit suicide and knew that the man his parents basically sold him to had effectively arranged the entire thing.
-Having to live under and follow the orders of the scumbag responsible for his parent's death, all the while aware if he slipped up he could be eliminated himself. In other words unless he was the good heir to Gendo Makashima his worth would cease to exist.
-Had to deal with realization that society at large didn't care and the only way he could deal with these injustices was to do something about them himself. Plus of course not exactly being able to overtly go traitor on Chronos' schemes that made Gendo look like a small time crook in comparison. Agito knows enough to be familiar with the whole zoafication effort and how little can be done about it.
-Has had a large slice of humble pie shoved down his throat repeatedly against various Hyper Zoanoids and Zoalords. Didn't give up despite this.
-Had his de facto surrogate family largely killed with the only one left doomed to die in a few years.
And you know I can go on.
The audacious thing for Takaya would them to have a confrontation where this was pointed out and Sho realized that inaction can have a higher price then action, at the very least.
- quoted from IC Ominae, Japan Legend forum.