I've only been a serious ENWorlder for a couple of years and, being in the UK, have had no exposure (yet!) to either GenCon or the ENnies, besides what's shown on the site. However...
What surprises me most is the underlying thread to this discussion, and I think it was actually said in not so many words in one of the earlier posts: 'If we are to be taken seriously as an award, we have to change.'
I wasn't aware that the ENnies weren't taken seriously. Most publishers who receive one prominently display it on their web site (hell, Malhavoc have had an ENnies medallion on their site for as long as I can remember). The shortlist announcements and results are met with much trepidation and excitement in all of the roleplaying circles I mix in. The very first thing I wanted to do when I found out about the Dragonlance Bestiary's silvers was mail my congrats to the authors, whom I work with regularly. There is already prestige and cachet in these awards. Unquestionably, they have become one of the most respected awards on the scene (as far as I'm concerned, the most respected), for many and varied reasons many of which are being analysed here. I just hope that 'reinventing' the ENnies doesn't detract from the very reasons why they have become so respected in the first place.
And that's all I wanted to say really.