Does Phantasy Star remind you of any particular books or authors, especially in the science fiction and fantasy fields? The games obviously have a really strong sci-fi feel throughout the series, so a lot of that stuff had to come from somewhere. Asimov seems pretty likely, with his stories about computers controlling the environment and going awry.
For some reason I've always gotten a strong Gene Wolfe and Ursula K. Le Guin vibe from Phantasy Star. Wolfe because of the darker themes, I guess, like the weird psychological/genetic relationship between Nei and Neifirst, and the idea of a poor android like Miun wandering in the desert and deteriorating, both physically and psychologically.
Phantasy Star also has really strong environmental themes, like Le Guin. Even in the first one Lassic was ruining entire regions with poison, and PS II was almost entirely centered on environmental issues (along with ideas of governance, which are very Asimov and Wolfe-like). There's also a big social science fiction element, with the examination of Nei's nonhuman status and the questions that it entails.
So I'm sorry for rambling here, but for some reason I've been thinking about the influences behind Phantasy Star. I feel like the series was pretty progressive when it came to its storylines.