"Actually, some of the cinemas 'frames' seemed to be copied from other Japanese anime and manga. Armen had some really interesting comparisons. Don't remember the link. He should chime in and post."
The creator of the original Lunar is Kazunari Tomi, who had worked for Nihon Falcom, on Ys and Sorcerian in the mid 80's, before creating Studio Alex with Kei Shigema.
Shigema had connections with the animation company Gainax. That's how I think they decided to hire Toshiyuki Kubooka as character designer (who was an animator on the series Nadia the secret of Blue Water or the movie Royal Space Force.)
Gainax was an animation company who also produced video games like the Princess Maker series, Gotzendiener (with studio Alex) or Alisia Dragoon (with GameArts).
Tomi having worked for Falcom, this can explain why there are elements in the opening of Lunar which are close to the opening of Ys like the camera shot with the monsters panning up to DarkFact/Ghaleon. There are also several shots which are almost carbon copies of scenes found in the opening of the anime Zillion.
The flying city of Vane in Lunar is also reminiscent of the floating city found in Ys. All this flying continent thing found in jrpgs since the 80's have been inspired by the anime movie Laputa made by Miyazaki. The same thing can be said for the airships found in almost every japanese RPG.
Also, the chocobos found in the FFs, were inspired by creatures found in Nausicaa.
But for the reference of Ys found in Lunar, it goes even further. Adol is actually in the game at the spring of transmission. In the original japanese version, theres a lonely character who isn't named, but who tells you he's a wanderer and that he had already seen during his past adventures a flying city like Vane but doesn't remember where it was.
http://img857.imageshack.us/i/tssj087.gif/In the US version, there's no reference to this, and the character appears like some kind of idiot who asks about how many licks it does take to get to the center of a tootsie roll pop (?)