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I'd recommend Nadia: the Secret of Blue Water. It's directed by Hideaki Anno (Same guy who directed Evangelion and was what led him to create it) and has a really interesting story. Only downside to it is there's around 8 episodes where Anno passed off directing to one of his friends and he bombed the fuck out of it. Other than that it's got the early 90's animation style you're looking for and an interesting story. I personally give it an 8.5/10.