I am a huge fan of games with a cute aesthetic that belie complex mechanics and high difficulty. Atelier does this with its alchemy system; creating strong gear and items is not a straightforward process. You're expected to think of any roadblock as a puzzle to be solved rather something you grind through or just buy better gear for. There are so many different variables in the alchemy system that I've spent hours thinking up creative ways to beat superbosses, while that's something I've never gotten to do with any other game. In a similar vein, I also enjoy roguelikes because you are allowed creativity in how you approach different situations.

tl;dr: are there any similar games (cute aesthetics optional, if it's a great game I'll play it anyway) with systems that force you to think and get creative with the game mechanics instead of just fight your way through everything?