[Shuuda]

the only thing that came out of the entire geass order is the fact that that Charles was immortal, and Lelouch had killed a bunch of children.

You forgot to add that the Geass cult stuff was also a factor that lead to the OoBKs betraying Lelouch, and V.V dying. So the Geass Cult stuff did matter.

The problem of having only good characters is quite simple

Scheinzel and Lelouch are neither good or bad, only human.

instead of Schneizel, and Lelouch seeking peace, they instead seek war,

And isn't the real world the same? People cannot agree with each other because of their different views. They don't seek war, they infact seek peace, but their conflicting methods and views on peace cause war.

Schneizel didn't feel like a final boss

Because their is not "Final boss" in Code Geass, and if there was one it would be Lelouch, who made himself into the villain.

Also an Anti-villain isn't a unique character that's why TV tropes has an entire page of them.

There are countless characters in the history of fiction, you cannot possibly expect each one to be completely unique, that's just impossible. Heck I bet that even Micheal Wilson is not a completely original character, he probably shares traits with many other character, but put together in a combination that may set him apart from the other who inspired his creation. In my opinion, Scheinzel comes under the Affably Evil trope, though I wouldn't say that Scheinzel is evil.

If Schneizel or Lelouch where actually in office, both would be out of office by the time their term limit was over for being incompetent people who tried to force their ideas on other people.

All leaders try to put their ideas into other people, it's called propaganda, and most people fall for it as well.