Well, 'Neon Genesis Evangelion' is extremely popular. It has a unique take on mecha - based science fiction, with complex characters and a deep, often philosophical story that delves into the nature of humanity and existence in a world under threat from mysterious beings.
Akira is quite popular too. Set in a post - apocalyptic Neo - Tokyo, it shows a world filled with advanced technology, psychic powers, and political unrest. The animation is iconic and it was one of the early anime that really brought Japanese science - fiction anime to a global audience.
In my opinion, 'Mobile Suit Gundam' series are also very popular. There are multiple series within it. They mainly focus on the battles between giant mechs in a space - opera - like setting. The series also explores themes like war, politics, and human relationships within the context of a science - fiction universe.