I have looked at quite a bunch of amazing games, and I've managed to write down a few patterns I've seen in them:
There's a focus on exploration. This is the core of the Metroidvania genre.
Autonomy of the player. Having the player seek out progression in the game with intrinsic motivation.
The antagonist is usually resembling of an abstract concept: An illness, a shadow, an (intense) feeling like grief, hopelessness or anxiety.
A cute and/or simple artstyle, where you can tell a lot with little.
The visuals usually have bright colours and a lot of contrast, as well as unnatural elements with nature as a base.
There's deep, dark themes like death, religion, an illness, conflict, war, end of the world, etc.
It takes place in an (ancient) huge abandoned kingdom or world, so the player feels a sense of smallness.
The soundstracks are stunning.