I laways think FLCL and Abenobashi Mahou Shotengai are the top anime series from GAINAX, while EVA is just... good enough, but nowhere near the greatness of FLCL and AMS
Well, I also think Gunbuster and Nadia: The Secret of Blue Water were quite great if we talk about their past works...
Anyway I love most of GAINAX's works, and have high expectations of them, but it's definitely not because of EVA.