Being in charge of the Hugos is always a thankless task, but this year I suspect it's more thankless than usual.
The administrators have released an FAQ answering some of the big questions many people have been wondering about. Looks to me like they did a pretty good job of dealing with some very difficult situations.
They definitely made a couple of mistakes, no question. But they also navigated gracefully through tricky waters in a couple of areas.
In particular, the controversial John L. Flynn story is permanently off the ballot. Quick recap: Flynn's story (published in a little-known online magazine called Nexxus) appeared on the initial ballot; it was discovered that Flynn's story had (according to his web page) appeared in a collection of his short fiction published by a small press in 2000, and was thus ineligible for an award for stories first published in 2002; Flynn claimed that the book had actually not become widely available until 2002, and thus that the story did not really appear before that year, and was still eligible; however, it turns out that the collection received 7 nominations for the Best Related Book category of the Hugos in 2001, suggesting that it was available enough to be nominated in 2000. (Seven nominations may not sound like many, but it's as many as J. R. R. Tolkien: Author of the Century and L. Ron Hubbard Presents the Best of the Writers of the Future received.) It's been a big mess all along the way, but the Hugo administrators have made a final decision, with no appeal available, so that's all behind us. Whew. As an editor of another online magazine that published Hugo-eligible fiction, I don't feel comfortable making further comments on the situation in public; I'll just leave it at saying that I approve of the Hugo administrators' decision.
Other decisions include putting Coraline in the Novella category rather than the Novel category and leaving Lilo & Stitch off the ballot. Although I was very sad not to see Lilo & Stitch on the ballot, I now think I understand what happened: it looks like it may've been a victim of the new long-form/short-form distinction. Since the movie was under 90 minutes long, some people quite reasonably listed it under short-form. The Hugo administrator is explicitly authorized to move a work to long-form if it's not below a certain length, and in fact decided to do so with this movie, so the system was working up to a point; unfortunately, many people put L&S in short-form and nominated five other things in long-form, and so those people's nominations of L&S couldn't be shifted to long-form. I don't know for sure that the movie would've made the ballot if everyone who nominated it had nominated it in long-form, but I wouldn't be at all surprised. Sadly, even though this is a case where I'm unhappy with the result, it's clear that the adminstrators did exactly what they were supposed to do, following both the letter and the spirit of the rules; this is a case where nominators not being aware of certain nitpicky details of the rules and of how they might interact may well have cost a good movie its nomination. Then again, it's entirely possible that people wouldn't have put L&S on their long-form ballots even if they'd known they could; no way to tell. Alas.
Anyway, looks to me like the administrators did a good job overall under trying circumstances, and I'm very glad to see their explanations made public.