This structure is pretty much the current Atelier system. If you wish for more plot and progression (and a slightly lower emphasis on crafting), try the Dusk trilogy (Ayesha, Escha & Logy, and Shallie) or the classic PS2 era ones (Iris trilogy and Mana Khemia).

Escha & Logy is the closest to the modern style, with separate small events and a lot of character bonding, while Ayesha and Shallie are a good bit more plot driven. Just note that these are older games without the quality of life aspects that are present in more recent titles. Also note that Ayesha has a fairly strict time limit, it's not too hard to hit for the main story but requires careful planning and mastery of a very obtuse crafting system to get all the side stories.

If you wish to try something a bit more traditional RPG-ish while still having the similar look, try WitchSpring R.

Honestly? Its kinda what Atelier is for the most part. It is a game series built around a crafting loop that primarily has very little plot narrative and a heavy focus on getting to know the characters, their lives and quiet slice of life moments with everyone. Its been this way more or less since the start.

Some will have more plot, others less. But generally the core has remained the same since the very first game with Marie. Atelier Ryza, and the Ryza Trilogy as a whole, tried to focus more on a narrative plot to make it feel more like a tradtional JRPG. IMO Ryza 1 did a lot of skipping over the character interactions that older Atelier games, and even later Ryza games, did a lot better.