More on Why Suzaku Later Joined Lelouch

Comparison between Lelouch and Suzaku is not about who is right or wrong, but rather about different values and principles.

Both of them live and do things in accordance with their values. Both of them want different outcomes.

Lelouch is villain according to Suzaku values. Lelouch could not care less if he is considered villain.

Suzaku is an idiot according to Lelouch values. Suzaku in turn could not care less if he is considered idiot.

Ultimately Suzaku is kind of person who wants to protect lives no matter what. That is why he serves the system and opposes any insurgency. Due to believe that war takes lives so it is bad and must be stopped no matter what.

By the end of R2 even he realized that protecting the system and opposing war does not guarantee saving lives.

That Lelouch and Black Knights are also a product of the Brittanian system. They are natural reaction to what Charles and Brittania was doing. They "Reality's answer to you." as Lelouch put it during the C-World Ragnarök Connection episode (20 or 21). They are the result of cruelty that Charles showed to Lelouch and the Japanese. 

Later Suzaku too realised that just eliminating Zero and Black Knights would not address the fundamental issues in the system or reality that created them in the first place. Without Zero there will be some other rebel leader to lead them against Brittania.

Thus, essentially letting Lelouch or Zero rule and fix the system is the only way forward that can actually end the fighting and save lives.

Suzaku and people like him are hard for someone like me to understand, so I could not fully recreate his reasoning in siding with Lelouch until recently. I said they made some sort of deal. Anime did not give us any details unfortunately. 

It is the same with our real world. Increase in crime is a reaction to austerity. Alt-right and cruel 'women exploiting' porn is a reaction to feminism. Reality answer to the bullshit they had done in 2008. That will only get worse unless they change.

In history there are similar examples. For example, Hitler and Nazi party only have to power as a reaction to the Great Depression and Economic Crisis or 1929. They would have been a footnote in history if economy did not collapse in 1929.