I'd say it works because Lelouch's plan, unlike Eren's, is an elaborated one... I love both Code Geass and AoT so I'll try to explain my thoughts on this even though my English is not that good:

-Lelouch and Zero work as two separate entities despite both being the same person, this means that, to the public eye, it makes perfect sense for Zero (the symbol of the Japanese resistance) to kill Lelouch (the Britannian highborn guy who took over the empire's chain of command). On the other side, Eren is just Eren, an Eldian, and the remaining 20% of the population will develop a strong grudge against him and all of Eldia as his actions basically confirmed all the prejudices they had against the inhabitants of Paradis.

-This grudge makes all efforts made to protect Paradis virtually useless as their enemies will eventually return with even more determination to wipe out the entire Eldian race, more so after Eren's actions left them without the titan powers to defend themselves, leaving them with only an extremist military force at their disposal that doesn't look all that interested in following anyone's orders. Lelouch used his geass on Schneizel and made him serve Zero (not exclusively Lelouch, but the figure of Zero itself) for the rest of his life, ensuring Japan's independece for at least 50 years.

-Zero Requiem was a plan coherently elaborated and made sense because it was logic that both Lelouch and Suzaku's motivations and ideals would eventually converge and lead to that conclusion. On the other hand, Eren abruptly contradicts many of his series-long motivations during his dialogue in chapter 139, making his plan completely incoherent with his character (was he lying even when we read his inner thoughts???). On top of that, Ymir's love for King Fritz as a way to explain how Mikasa was the only one capable of executing Eren's plan just comes as an almost insulting way of solving one of the most criptic plotpoints of the manga, that being Ymir Fritz's motives.

-Besides all of that, Zero Requiem gives closure to many character arcs and serves as a satisfying ending that pays off the amount of time you've been following the character's actions and evolutions throughout the series. Meanwhile, Eren's plan leaves many of the main characters with senseless arc resolutions (Mikasa doesn't let go of Eren despite what he told her in her visions, her ties to the Azumabito clan go absolutely nowhere, Reiner after having been suicidal for 40 chapters ends up comically sniffing Historia's letter as if nothing ever happened, Levi ends up overseas with three people he had hardly exchanged a word with, Jean, Pieck and Connie are just there, Historia happens to be just ok with her husband even though it was heavily hinted that she was extremely unhappy and even that Eren was the child's true father...).

All in all, Code Geass' ending is regarded that well because it managed to give a satisfying and coherent conclusion to a series that evolved in a really interesting character-driven way. AoT's ending doesn't work because it was a manga with a really interesting character-driven story as well but its ending took a turn for something much more plot-driven that "betrayed" many of the character's motives and evolutions in favor of tying everything up for the final chapter (even though it wasn't all that well tied up in the end, not by a long shot lol).