The problem is that there is a bunch of server configuration beyond simply deploying the app.
The most basic cases consist of copying JDBC jars and creating connection pools etc.
But add in JMS queues, Security Realms, a slew of Virtual Servers, etc., and upgrading is more than simply reinstalling the server and plopping in your application. And the admin GUI is adequate for simple tasks, but not for doing lots of things in bulk.
There was at one time the ability to migrate using asadmin, but I don't know it that's well supported. At a minimum, it doesn't work across releases of the same version of GF, so it's kind of a pain.
Thankfully, the domain.xml hasn't changed dramatically from 1.x to 2.x. Another thing I would suggest is creating a new domain, with a default domain.xml, fire up the domain (the server will load and rewrite, and specifically reformat, the domain.xml file).
After you've done that, you can DIFF the stock domain.xml vs your servers domain.xml. Your major elements should drop out pretty readily. And you can use that new set as an inspiration to hack the domain.xml file directly on the new version.
But, yes, it's a pain right now.
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