Following are the difference between Java FileChooser and native file chooser,
This includes Look and Feel differences and Functional differences


 1) Fields "Look in", "File name", "Files of type" are showing mnemonic in
  there corresponding labels, while in case of Java File chooser mnemonic is
  working but not shown as underlined in dialog.
 2) There is a extra field named "Encoding" is present which allows u to select
    file's encoding in native this is not present in java file chooser.
 3) File name field is using editable combo as control, while jfile chooser
    uses simple textfield.
 4) "Go to last folder visited" button is not present in java file chooser which
    is present in native.
 5) In native go to folder where user dont have permission to create folder
    and try creating folder, it will give you proper error message, now
     repeat the same with java file chooser, and folder will not be created
     and nor any error message comes up.
 6) Java File chooser doesn't support wild card '?', So if user wants to
    display all files which matches this wild card, he cant do this in Java
    file chooser, while native do support it.
 7) In Java file chooser, Click on details to see extra information of files
    and folders in tabular format, Now this table can't be sorted by any of
    the columns. While sorting is present in native which really very helpful.