The terrorists are entirely justified in their violent resistance against the obviously evil and genocidal Britannian empire, which is something of a stand in for both the British Empire and the US.
The annoying liberal deuteragonist bumbles around for 2/3 of the show being a supersoldier for the Britannian Empire while constantly making these bizarre self righteous arguments that Lelouch's rebellion is just too darn mean and violent, we have to support the Britannian Empire's rule of law just a while longer guys! The longer this goes on, the more and more his world view crumbles around him as basically nothing goes to plan for this liberal who is just incapable of grappling with material reality. He ends up following his sense of liberal morality all the way to accidentally killing millions with a Britannian wunderwaffe nuke. This leads him on his jokerification arc wherein he realizes the error of his ways and actually supports Lelouch through the batshit last few episodes of this show.
Anyway, I can't recommend this show to anyone in year of our lord 2024 because it's obnoxiously, embarrassingly horny in a very mid 2000s anime way, because that's exactly what it is. But I'm imagining what could have been.
I think that kinda reflect the core message of the show, which is pretty libby, though. "society is bad because of bad people, and you can totally just simply wish them away". At the end of the day, all evils can be fixed by magic. From the imperialistic empire, monarchism, fascism, capitalism and classism can be fixed by just magic them away with your command. It smell a lot like the liberal enlightenment centrist idea that everyone but them are know the truth and that the truth will destroy every opposition regardless of material conditions.
Even before that, Lelouch's comrades who is a pretty mixed group of different nationality just give up on him when he lost his mask and reveal that he had been a Britannian prince all along. Sure there were other mistakes that he made that lead to a bunch of genocide and loses before that, but I don't remember his comrades (outside of Kallen, his lover) even let him explain. This spoke lowly of the capability of revolutions and freedom movements by showing them as a bunch of morons who are just led by conman that's just one revelation away from getting lynched.
See, I disagree because the events I described in my comment are not actually the conclusion of the show. Nothing is inherently solved by the death of King Charles. What killing King Charles actually accomplishes is that merely Lelouch has one less enemy so he can focus on stopping his brother Schneizel, who represents a much more competent threat than his father did, one with the connections to build the Sword of Damocles. Lelouch does ultimately use his geass to neutralize Schneizel, but he is only in a position to do so because a war is fought that spills an unfathomable sea of blood, and that is where the big shift in power structure comes from that allows for the effective revolution we see toward the end.
Now, the very existence of geass magic fundamentally divorces the world of Code Geass from ours, but I thought the Black Knight reaction to Zero's identity and the power of Geass made a lot of sense. Learning about the very existence of geass is such a mind fuck because being put under the command of Lelouch's geass is an extremely gross violation of bodily autonomy. It's a serious crime to use it in such a way that isn't directly advancing the goal of the proletariat in class war. Lelouch's identity as a Britannian prince isn't what necessarily loses him the support of his comrades, it's his ability to violate people in such a way with absolutely zero accountability or oversight. They also learn that Euphemia's massacre of the Japanese people was orchestrated entirely by geass, Lelouch never tells anyone but CC that it was an accident.
They all start to question whether their very involvement in the resistance is their own will or not. Kallen is the only member of the Black Knights to give Lelouch a chance because she is the only one who knows him personally enough to continue trusting him. Which is ironic because Lelouch did in fact use his geass on her previously, as minor an order it was.
There is two problems with this conflict though. Firstly, the way that Lelouch built a resistance against his brother was not to win back his old allies and prove to them his trust worthiness, but by magically flip the whole chessboard and turn every Britannian into a mind slave willingly do his bidding. That sounds exactly like liberal fantasy fixing the system and transform it into a force for good. Secondly, Schneizel also did a board flip and get everyone on the rebel group to support him as their leader for a war which essentially is just a fight for the throne of the world. The rebel even complicit in a nuclear first strike attack on the Britannian capital which have unknown number of civilian in it.
This plot point however shine the spot light on the structural problem of the whole rebels. They are just a bunch of people with no unified ideology that can let them look pass the fear of the power of geass to even offer Lelouch a chance to explain himself. They don't even offer him a real trial before trying to gun him down in cold blood. While I'm sure there are many example in real life where people flipped out and assassinated their political leaders for less. The story decision here to let Lelouch be saved not by the quality of his ideology, or any of his policies but just purely because another broken and exploited character clung onto him and bailed him out with their life speak a lot for the quality of the rebels leadership and ideology.
That's my main problem with Code Geass to be honest. Overall, it's an entertaining show with the facade of anti-colonialism, anti-imperialism, pretty twisting story line and some awesome mecha battle. However, the show stop short of offering any true solutions to the problems and instead just outright prescript great person theory and enlightenment dictatorship to imperialism. It doesn't even have any representation for communism, anarchism or any more leftist groups. Instead, we had an imperial capitalist monarchism vs a bunch of nationalist monarchist of a different religion vs some liberal democracies in the background.
I agree the show, especially toward the end, is definitely no kind of masterpiece, and many of the plot points are definitely really dumb, just in a very entertaining way. You're correct that the fact that Lelouch almost died because his cadres didn't have a real shared ideology that would allow for them to have any kind of faith or respect in his leadership doesn't quite work as a criticism of exactly that kind of organization when Lelouch uses his geass to win anyway by mind controlling the remainder of the Britannian Empire's armed forces.
My being impressed at this show mainly comes from the mere fact that it's very explicitly and wholeheartedly endorsing violent resistance against US coded imperialism. I feel as if that's rare from popular media, especially back when it released. It neglects to take a specific political stance, but it's absolutely anti-imperialist, even if just being that is a low bar to clear. The rest is mostly very fun but harmless anime slop apart from the parts I criticized in the OP.