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Yui Ichijo
In Sadamoto's artbook there Mond you can find the first concept art of Evangelion's characters.
Rei was very different from the one we know: more Japanese-like, she had black hair and black eyes.
Also the first version of plug-suite was really different but for the color.
In a sketch we can also see that her name too was different, infact it was Yui Ichijo.
It looks as it was another tribute to another series character, Hikaru Ichijo from Macross.

The word "Rei" written in katakana as a person's name means "Spirit".It's also a male name.
The word "Ayanami" is composed by the two kanji "silk" e "wave", and it can be translated as "Wave of Silk".
It was the name of a destroyer of the Japanese Army in WWII that was destroyed by the Allied float in 1942 during the battle of Guadalcanal.

Hideaki Anno's Explaination: "Ayanami is named after a ship of the former Japan navy. Rei is just a pun of ["Zero". The two words have the same pronunciation], but actually named after Hino Rei of Sailor Moon. It was a beit to invite Iku-chan [Ikuhara Kunihiko] as a staff, but he ran away. Too bad."
Source: Japan.Anime.Evangelion FAQ