Well, XML can be easily processed by 3rd-party-applications, like a graphical permissions editor as well as an graphical configuration editor. The positive side on XML is also the strict definition with the XSD and the ability to extend it easily. What you forget in your system is the ability to create user defined groups, which can inherit permissions from other group, exclude permissions and so on. If you don't like to type all these tags, you can simply write a config generator, I would do that too xP
Also, if I understand you correctly, if the default user has got the permission to build and use a hypothetical plugin warp:
permissions.user = ("mineserver.build", "plugin.warp.warpto");
If you assign many different permissions on one user, this format produces endless lines and sucks therefor pretty much.
You can always use some autocompleting software to write the config (MS XML Notepad 2007 on Windows, Eclipse with web extensions should do it on Linux) - can't be easier.
You always have to design a system for the DAU (German abbreviation for "Dümmster anzunehmender User", Stupidest user possible), and in my opinion, XML is best suited for this. I can easily write some applications for easy configuration and easy permissions editing.
Oh, by the way, some in-game commands to change permissions would be very nice. Like add users to groups, give groups additional permissions, create groups and so on.