You're talking out of your ass. Setting up a VM in VirtualBox is pathetically easy, as is exporting it to a single file (go to the file menu, click on "export appliance"), as is opening it ("VirtualBox --startvm foobar" or just use the GUI).
And the reason that VMs are not stored as single files is that that would be a really dumb idea. VirtualBox uses different files for CD images, hard disk images, configuration files and log files, so i can process the configuration file with xmlstarlet, the log files with grep and so on. Grouping files together is what directories are for; stuffing unrelated things in a single file only makes things more complicated than they need to be.