Firs of all XML serialization should be optional but not mandatory. Because owerhead is too high and XML advantages you are described is not always useful. I would say, that in most cases binary representation is more convenient. Especially for object machalling.
Now about File. I agree that file should be improved, but disagree about the way. File should represent some object on a virtual file system, and that VFS should allows to plug in custom FS, sucha s FTP, CVS, WebDAV and so on. Now we have to alternatives to access files - URLConnection and File. So, they should be merged and should allow more features and convenience.