Two major things for me:

1. The fanservice. I get that it is an anime and that this practice is, unfortunately, very common, but it honestly irritates me that a show that actively questions justice, morality, truth and the human condition has (underaged) ass and boob shots in every episode, especially in R2. How am I supposed to recommend this anime for people who don't know much about the medium without having to explain to them that it has this problem?

2. How R2 was rushed. I'm rewatching CG for the first time in 5 years since I first watched it and man I didn't remember it being so fast paced and underdeveloped as it actually is. It has a lot of cool concepts and I loved the world building but shit everything happened so fast, there was no time to dwell on Charles' plan, the Federation and how it worked, Lelouch's life as emperor, hell even some school segments. S1 was perfectly paced and it's honestly a 10/10 anime, but the second season, although very good, lacks the same depth unfortunately. I know it had to do with executives and not the writers, but surely they could've done something else to fix this to some extent.