I haven't played a lot of Atelier games, but I have a mixed relationship with the series. I loved Atelier Iris: Eternal Mana. Veola, the magic shop clerk, has one of my favorite JRPG character stories. Killer soundtrack too. I still play the Deceitful Wings guitar arranged album during my commute.
The only others I've played are Atelier Annie (which I reviewed positively for the site), Mana Khemia (which I simply could not get into), and the first Ar Tonelico (excellent music, but I couldn't get into that game either.)
It is a series I'd like to return to someday. Though, like my homegirl Dice, I prefer something more in line with Iris than Annie.
And as an aside, Marie is one of the best looking JRPG heroines http://www.game-ost.com/static/covers_soundtracks/1/5/15537_840252.jpg
Mixed feelings about this franchise sums it up nicely for me as well. I too am on the "Iris" side of the coin.
Thing is, the Atelier series in very peculiar for me in a certain sense. That is, when I think about what the more traditional Atelier games concern themselves with and reflect on the mechanics they don't entice me. However, once I am actually playing them I couldn't be more engrossed. Even Rorona (which I couldn't stand for a lot of reasons) had a certain "hold" on me that kept me playing to the end and even caring a great deal about what ending I got.
This is usually the complete opposite for me... Typically I find myself being enticed with idea of a game, only to be let down with the actual experience.
One thing is for certain though, when it comes to art and soundtracks the whole Atelier universe and spin-offs are a cut above in my book. I really wish Gust would apply such talents to more Epic/Traditional games as an aside to the Atelier stuff to be honest.
And for the record, I do certainly feel that if Ar Tonelico were dubbed "Atelier Tonelico" no one would have questioned it.
Lastly (since you brought up shop keepers), I want to throw out a little "Pamela" love. Not only a fav shop-keeper, but a spectre to boot!