Ctrayne: Considering the history of the Ys series, I'm surprised to hear you say 6 and 7 have weak plots, since along with 5 and Origin, I feel they have some of the best and most well-written stories in the entire series. 6, in particular, is an oft-unsung gem in that regard, as its plot is multilayered, connects brilliantly with plot threads introduced in Ys IV, and has excellent characterization throughout.
I'm also not sure how you can say their games aren't "dark" anymore, unless you're going SOLELY by art style. Ys Seven had one of the darkest plots of any Ys game, and the entire Kiseki series is so dark and disturbing in some of its plot developments that it actually reaches (and even surpasses) Dinosaur levels at times, and completely blows away anything from Xanadu Next.
Heck, even Zwei II gets so dark as to be disturbing in parts -- and in that case, the cutesy art style enhances the atmosphere, making the dark/disturbing sections of the game all the MORE dark and disturbing. Personally, I love it when cute things are put into decidedly un-cute situations, and feel this is a great way of making anything much more moody and memorable.
If your concern is merely art style... well, then I guess I can't exactly argue. But just because something has an anime art style, or even a CUTESY anime art style, doesn't preclude it from being dark and atmospheric. Just look at Corpse Party.