The 6 Atelier games I've played are separated in to two umm "series". Atelier Rorona, Totori, and Meruru are part of the Atelier Arland series and each take place a few years after the other with the protagonist of the previous game being the mentor/teacher for the current protagonist. Ayesha, Escha & Logy, and Shallie are all part of the Atelier Dusk series.

The games do center around alchemy and all (except for Shallie) are a combination of RPG and time management game of sorts. Shallie did take out the time limits and stuff though. The Arland series is generally more upbeat and follows each heroine's personal journey. Rorona is stuck taking care of her Master's Alchemy Atelier so it doesn't get shut down. Totori is serching for her missing mother, and Meruru is trying to expand her Kingdom so her father will let her become an alchemist.

The Dusk series is a bit darker and is actually about a world on the verge of death because of people abusing alchemy in times past. Ayesha is searching for her missing sister, Escha & Logy investigate some ruins from these times past, and the Shallie's (there are two, Shallistera as you see above and Shallotte) trying to find a cure for the drought spreading around the world.

In both games you use alchemy for items. You make your healing items this way, accessories, attack items, etc, as well as you'll usually have requests and such to fill using alchemy.