R1: No Euphemia/Massacre princess incident.
I'd have Schneizel fuck everything up from the shadows, destroying the idea of the Special Administrated Zone. Somehow Euphy dies in an accident, but still, Zero is somehow blamed.
Suzaku discovers Lelouch is Zero, Nunally is abducted, we have the Lelouch-Suzaku confrontation in Episode 25.
This time around tho, Kallen doesn't run away. She saves Lulu from Suzaku, but in the process Zero is mortally wounded.
R2: A year later, we find Lelouch has been in a coma. Kallen and C.C. have been taking care of him. C.C. has tried to wake him up several times, failing every time.
Suzaku discovers the place where Lelouch is being hidden, assaults it, and somehow C.C., Suzaku and Lelouch go into that mind rape thing that happened when C.C. tried to save lelouch from Suzaku in R1 (when she touched Lancelot, and then Lulu touched her).
Lulu and C.C. discover (via Suzaku's memories) that Nunally is in Britannia, with the emperor. Suzaku finds out Zero never did a thing to Euphemia.
Lelouch wakes up, Suzaku is attacked by Kallen and knocked out. Lelouch tells her not to kill him.
Lelouch saves the OotBK that are about to be killed. After a few months, they do the MILLION ZERO's plan and go to china.
Important changes: Suzaku is not a knight of seven. Due to finding out what happened, he starts distrusting the empire.
No more School shit episodes. Yet, Shirley, Rivalz and Milly will still be shown from time to time, due to them having an important impact in Lelouch.
Also, no Rolo.