Chiho Saito's Utena manga is considered vastly inferior to the anime for a number of reasons.
Whereas the anime, created by Be-PAPAS, is a display of bizarre symbolism and amazing character development, Miss Saito's manga starts off with Utena at a regular high school with a best friend who has a crush on her. In other words, it's disturbingly traditional shoujo fair, and half of the first volume is spent before Utena arrives at Ohtori Academy.
A good example of how this affects the plot is found in one of the main characters, Miki. In the anime, the tension between Miki and his twin Kozue, who wants to have an incestual relationship with him, builds throughout the series. Miki, however, falls in love with Anthy... largely because she reminds him of who Kozue used to be. The delicate irony of this situation is a pleasure to watch unfold.
In the manga, however, Miki likes Utena and keeps stealing kisses from her when she's asleep; Kozue gets jealous and then she is kidnapped; Miki and Utena have to fight each other as a result. The reasoning here is clunky and while it makes for a good shoujo read, it isn't up to the standards set by Be-PAPAS.
In her defense, however, Miss Saito began the manga at roughly the same time as the anime began, and she was told very little about the director's vision for the series. I assume this is why her story varies so much from its vastly more mature counterpart. Saito's art is also very beautiful and worth looking at despite the inconsistencies with the series.