EDIT: After reading a MS Connect article, it appears that .Net 2.0 has a ‘feature’ where it makes ObsoleteAttribute equivalent to XmlIgnoreAttribute without any notification in the documentation. So I’m going to revise my answer to say that the only way to have your cake and eat it too in this instance is to follow @Will’s advice and implement serialization manually. This will be your only future proof way of including Obsolete properties in your XML. It is not pretty in .Net 2.0, but .Net 3.0+ can make life easier.
From XmlSerializer:
Objects marked with the Obsolete Attribute no longer serialized
In the .NET Framework 3.5 the XmlSerializer class no longer serializes objects that are marked as [Obsolete].