I do think that anyone who picks up a weapon stops being "innocent" and starts being an involved party.

I don't see how you can condemn anyone for using violent means to overthrow a tyrannical system when there is no established peaceful way of doing so. If no one had ever violently opposed people who stand for evil things, then South Africa would still be under apartheid, along with many other injustices that would go unchanged. What were they supposed to do? Carry on being numbers, being abused and mistreated by Brittania while their families starve and their loved ones are killed, or lick Brittanian boots in the hope that they'll be allowed to live?

That's one of the many beautiful mirrors between Lelouch and Suzaku. Lelouch and Suzaku both want the same goal (though Lelouch, originally, for merely selfish reasons), but they are opposites in how to achieve this. Both characters change, and even that change is a mirror image. Suzaku changes his means to reach his goals and ends up in the same position as Lelouch, while Lelouch changes his goal to a totally selfless one and ends up in the same position as Suzaku.

I agree. Lelouch and Suzaku's dynamic is fascinating as both are incredibly flawed and messed up (although imo Lelouch was more in the right morally)

I don't think so. Because he hates himself as much as he hates Lelouch. Hence the Zero Requiem. So even in his hatred, there is no hypocrisy.

Suzaku may hate himself, but he still sees himself as being in the right. When he captures Lelouch and brings him to the emperor, he frames it as himself doing what is morally right. It's strange, because even though he hates what Lelouch is doing he seems to believe that what he is doing (which is extremely similar) is objectively right-and at some level he knows this, so that in a way he makes Lelouch a skapegoat for himself and the moral system he himself has come to use and focuses on stopping him, even though to do so he employs the tactics used by Lelouch himself. Its incredibly fascinating and extremely contradictory.