they are only storing key:value pairs. But how would I save a nested object?
What is nested object? You can store any object that can represent by JSON (or more correctly serializable by structured cloning algorithm). Is that nested object? You can convert any OOPS into JSON and get it back through its construction. For XML, just store serialized string format.
If you refer relationship, it is different question. I have write a bit about IndexedDB relationship. Modeling a relaionship in IndexedDB is not a problem. In fact, it support very well.