I think fusangite nailed it. Anyone can send in a link. So what you get is any Tom, Dick, or Harry sending in a link for their one podcast they've ever made on something to do with RPGs because they think it would be "cool" to get an ENnie. But the wouldn't really care if the didn't because all it took them was copying and pasting a link and clicking send. The judges would be obligated to listen to that podcast. I can imagine that causing an overabundance of really bad podcasts that are received and a huge feeling of wasted time on the part of the judges.
By changing the rules to force people to send in 6 CDs, it weeds out the "this would be cool" people and only those who truly care whether or not they earn an ENnie will send them in. The judges don't feel that they're wasting their time because they know that they are getting quality podcasts from those that think the ENnies are a truly worthwhile endeavor.
No matter how you want to rationalize it, no matter how much you don't like the changing of the rules, it all boils down to this: If you truly, truly cared about the ENnies, if you believe that winning an ENnie is an honor and something to be proud of, then you would have burned the CDs and sent them in. You would have done whatever was necessary to win it, within the rules of course, no matter how much you disagreed with the rules. If the only "principle" you're concerned about here is the fact that you have to put CDs into an envelope and spend a little money, then you have little room to complain. Honestly, that makes me think you're just cheap, not that you are sticking to some sort of "principle."