Games are hugely varied. No doubt there are games out there for which SQLite is perfect. But I wouldn't use it for making partial updates in something like Minecraft.

It's not practical to store individual Minecraft blocks as table entries, so if you were using SQLite, you'd likely just store chunks (e.g. 16x16x16 blocks) as binary blobs. Then you'd rewrite entire chunks on save. It's not really taking advantage of what SQLite offers.

There are a lot of serializers and frameworks out there you could choose from, but even something as simple as just writing one map region per file and overwriting modified regions on save would be better than SQLite.