and this is bad why? But it's actually more of a Gainax tradition
Actually a lot of the bunny girls were modeled on previous Gonzo characters
Back Row: Rei(Evangelion),Mahoro(Mahoromatic), Asuka(Evangelion), Lark(Gunbuster 2). With Nono(Gunbuster 2) in the front.
As for the Gainax tradition before they were even called Gainax the founders of the company made little animated segments for a Japanese convention called Daicon in the early 80s. If you google you'll probably find some of them. They did one for Daicon III which had a young girl leaving on a spaceship I think and then she reappears in their Daicon IV classic.
In the Daicon IV the girl has grown up into buxomy bunny girl who has super powers and fights against Darth Vader, Godzilla, and a lot of other sci-fi/anime/cartoon characters.
So basically it's all just a lot of Gainax being Gainax. They love to reference their first works and past works in their shows. Infact the bunny girl has popped up previous times. Haruko wears her costume in some of FLCL and even references Daicon.