I guess it isn't too surprising when the other games being compared to are all building on each other while Ayesha was somewhat of a reboot.
I personally am kinda ambivalent towards Ayesha. It had a lot of good ideas (synthesis skills!) and there were some outstanding pieces of music such as Recollection Hill, but the world concept kinda lent itself to homogenous, colorless environments and the skills and traits weren't powerful enough for me. Ayesha was still an enjoyable game for me, especially considering that I'm mentally comparing it to Meruru (the third Arland game vs. the first Dusk game) and Eschatology (the sequel).
But that's not it for me at all, when I compare with all Atelier games, I find I like earlier (Iris and Mana Khemia) ones much more than later ones, from later ones it would go something like this: Meruru>Totori>Rorona>Annie>>>>>>>>>>>>>>>>>Ayesha. It just feels a lot worse to me than any other game, locations are bland and boring, characters are no fun at all, even Sterk is somehow worse than in previous games and I liked him, plot is ... how do I put it, even worse than usual, dialogues are insufferable, and I had no such problem in other atelier games.
What I do like is alchemy, I liked alchemy skills, and if even alchemy system seems a bit convoluted, I still liked it a lot. That's why I can't say I hate this game, I just hope that new games will be better than this.