Single User Application File/Data Storage Recommendations

I currently have a C# winform application in which you enter data that is ultimately hierarchical. The amount of data being stored isn't huge. The original version used SQL CE to store the information. However, I found it to be quite slow. Also, I wanted to be able to save application files using my own extension.

I had changed my approach to basically keep my data loaded in-memory using class objects. To save, I simply serialize everything using ProtoBuf and deserialize when opening a file. This approach is lightning fast and changes are never persisted until a user clicks save. However, I find it a little cumbersome to query my hierarchical data. I query data using Linq-To-Objects. I'll have ClassA having a GUID key. I can reference ClassA in ClassB via the GUID. However, I can't really do an easy SQL join-type query to get ClassB properties along with ClassA properties. I get around it by creating a navigation property on ClassB to ClassA that simple returns ClassA via a LINQ query on the GUID. However, this results in a lot of collection scanning.

What options are out there that give me fast, single-user, relational file storage? I would still like to work in-memory where changes aren't persisted until a user uses File|Save. I would also like to be able to continue querying the data using LINQ. I'm looking at SQLite as an option. Are there better options or approaches out there for me?