The biggest difference is that three of the Inner Senshi, Mars, Mercury and Jupiter are kidnapped by the Black Moon. The Ayakashi sisters never turn good and all of them are killed by Sailormoon.

The Ann/Ail arc never existed in the manga

In the anime Black Lady is changed back to normal by Neo-Queen Serenity. In the manga she returns to normal after Pluto uses her forbidden "Time Stop" and dies

In the anime all of the senshi and Tuxedo Kamen travel to the future. In the manga only Moon, Venus and Kamen go.

This section introduces two new characters, Asanuma and Kotono, who never existed in the anime

Prince Saffir never turns good like in the anime. He is killed by Demando.

At the ned of this arc the senshi get new 'planet power" transformations that never existed in the anime.

In the manga the final battle with the Death Phantom is fought in the future.

Chibi-Usa returns to train as Sailorchibimoon before the S part of the manga starts.

Usagi and Mamoru never break up like in the anime and Mamoru never receives any dreams from King Endymion.

Usagi does not change into Neo-Queen Serenity when she fights Death Phantom