Flame: You're missing the point, sorta.
People change, my friend. Their viewpoints change, especially over time... and as we know, X is full of emotions, because he was created that way. He can make his own decisions. So what's there to stop him, from suddenly getting pissed at everything, and by everything I mean of course, all those goddamn Irregulars who keep causing harm? Considering he can make his own decisions, he can also make such decisions which are simply wrong. After all, nobody is perfect. Not X, nor Zero nor anybody.
So with that in mind, the plot of Tyrant X, can be done in many ways. Some of them might lead to failure (like the example I mentioned earlier) or they can be done right.
Heck, if you really want to, you don't even have to make X that much of a bad guy. You can make him even more tragic, by making him a character who created that horrible policy of Repliroid disposal, because he simply had no other choice, and was forced into it by the bad situation Neo Arcadia and humanity in general was in. In other words, make him do something he clearly hates. He's fighting for it, even though he knows it's wrong.
There are many ways to do it right, you just have to think. But as I said previously, we'll never know because LOL CAPCOM.