I like how these games have added a disclaimer saying where there are events. I am so tired of running around town every day in order not to miss an event. Now I can see the events right away and go there.
I'm glad to see they added flags for the events. With me it happened almost like you, I played most of Ayesha but didn't trigger a certain event which was necessary for the story to advance, when I finally managed to see it I had little time to do anything else and had to run through the story.
After this I decided to give the Atelier series some time to breath. Not much, I just think I'll wait for the Vita version of Escha & Loggy instead of getting the PS3 version. I might even try the Japanese version if I manage to find it at a good price.
Like you said, I don't replay them, at least not as soon as I finish them, so I like to give some time before going back to them.