Alrighty, Last volume of the manga (Finally) got released in the US. Story ends the same, few stupid things, The way the did the betrayal was much different this time.
[spoiler]That dipshit "This is a massacre" guy is still alive, and he tells them about the Geass Cult Incident, with Tamaki of all people being one of the first to be open to betraying Zero, Not Ohgi this time around (Because Villetta didn't exist till the R2 part of the Manga, so she and Ohgi never became lovers.) (No Diethard either, his lines were taken by Kaguya and his fate taken by Kanon (Somewhat, I don't think he dies but he is shot.)
Also, Anya isn't a robot (No Marianne inside of her in this reality.) Suzaku "Dies" from A [tornado fang]ing Sword in the back of his knee. C.C. is captured by the black knights after being held by Kallen at gunpoint (real smart) and is actually strapped into her Straightjacket for the second time ever.
And Finally, Villetta is the one who hosts Mariannes soul (Being a new security officer at that incident), what.
Overall, the story was handled slightly better in manga form than it was in Anime form. But only the R2 segment, the First Season is still superior to the Manga.[/spoiler]