One of the best Evangelion fanfics could be 'Those Women at the Water's Edge'. It delves deep into the characters' emotions and relationships in a very engaging way. It gives a fresh perspective on the Evangelion world and its complex characters.
Legally, it can cause problems for the franchise. Since it uses the Evangelion name and concepts without proper authorization in an inappropriate context, it could potentially lead to copyright issues. Also, it can limit the creative direction of the official franchise. If the public perception is skewed by this inappropriate fan fiction, it may be difficult for the official creators to explore new and positive storylines and expansions without first having to disassociate from the negative connotations created by the erotic fan fiction.
In general, the Evangelion mangas are considered good. They expand on the anime's universe, providing more depth and character development. However, it depends on personal preferences as some might find the style or pacing not to their liking.
The Evangelion Anima Story has a complex plot. It involves new battles against Angels and the development of the characters in a different post - Third Impact world. It shows the further evolution of the Evangelion units and the relationships among the pilots.