Wait. Okay, I did say that, but before that-- said I to myself "Self, it's been too long since you've written anything even remotely intellectualy on your blog, and isn't it about time you should change that?"
So I'm going to write something semi-serious about Dr. Horrible's Sing-Along Blog. (Cut for the courtesy of people who are sick of hearing about it.)
All right. Just so you know where I'm coming from: I really, genuinely enjoyed the whole series, even despite my embarassment squick almost getting triggered in Act I, and I think I'm one of the few people who isn't either completely shattered or utterly pissed off over the ending. This means that I might not be as hardcore of my criticism as I ought to be.
So, let's see, where to start. Probably would be a good place to start with Billy, because I think you can make a pretty good case that Billy is a Nice Guy (tm). Now, granted, he isn't explicitly whining that the universe owes him pussy because he's Such A Nice Person, Damn It. At the same time, however, I think it gets made pretty clear that one of his main motivations for trying to get into the Evil League Of Evil is so that he can impress Penny with his feats of villainy. (To me, this reads rather like "girls don't like nice guys like me, but assholes like Captain Hammer! So if I'm worse than him, I'll win her for sure!" More about this below.) I think the bridge of "Brand New Day" (sung right after he resolves to kill Captain Hammer to get into the ELE) makes this pretty explicit:
And Penny will see the evil me
Not a joke, not a dork, not a failure
And she may cry, but her tears will dry
When I hand her the keys to a shiny new Australia
This thread of the story conatins a tasty ironic center, of course-- Billy is too busy concentrating on his villainous plans that it simply doesn't occur to him that Penny might be a lot more attracted to somebody who's honest about himself despite his awkwardness . If he'd let go of his supervillain plans, gotten over his nervousness, and spent more time just talking to Penny (remember that Penny's waiting for Billy at the laundromat, with frozen yogurt no less, but Billy's standing her up because he's too busy working on his freeze ray to get rid of Captain Hammer, because as everyone knows, nothing wins a lady's heart more than killing her boyfriend), then things would've turned out probably happier for everyone. That's not to say that this kind of story doesn't have its own issues, but since that's now how Dr. Horrible turned out, those issues are something to save for another entry.
Now, Joss Whedon isn't lampshading that Billy is a Nice Guy. Rather, I think that what he's doing is something both more subtle and more hardcore than that. I think that Joss sets up the story so that by Act III, the audience is supposed to be sympathizing with Billy, hoping he'll become a supervillain, get the girl, and defeat the smarmy traditional hero. (This may be vastly at odds with your own personal feelings at this point in the show. Bear with me.) I think Joss might be counting on the audience putting themselves in Billy's position.
And so, how does Joss end the show? Well, like he said himself: "Dr. Horrible got everything he wanted. Billy didn't." Dr. Horrible is a solid member of the Evil League of Evil; Billy is completely alone and emotionally broken, because Penny is dead as a result of his own actions. And the way I read this is that Joss is sort of hitting us in the face with a clue bat -- saying "Being evil doesn't get you the girl, being evil just makes you evil!"
That's how I look at it, at least.
As for the criticisms of Penny's character: A lot of people on the Internet seem to think that those who criticize her characterization are a bunch of anti-fun harpies who shoehorn feminist issues into every little thing they encounter because they want to make everyone feel guilty and awful. And the way I see it, that's nowhere near the truth -- I think the people who criticize Penny for being a one-dimensional character (an idealized female image who basically exists only as a prize for the two male main characters to dickfight over, shows very little agency of her own, and who dies at the end only to manipulate the emotions of the audience) have a valid point. I'm still not sure whether I agree with the point wholeheartedly, but it's a point that deserves some serious thought.
And nobody's saying that Penny's characterization means that Joss Whedon is a big ol' meanie sexist who's never done anything good ever in his life and probably kicks puppies; what I see them saying is "We've seen this shit ten thousand times before, and it's way beyond getting old now." Which, when you get right down to is, is basically the same idea that drove the feminist responses to Laundrygate and Tentaclegate last year.
Finally, I've also read responses to Dr. Horrible that basically say that Joss Whedon doesn't know how to write endings. I disagree -- granted that I haven't seen too terribly much of Whedon's stuff, but from what I have seen (namely, Buffy and Firefly / Serenity, a lot of his stuff seems to end as "Riding off into the sunset, but at great cost." It's a happy ending, but it always comes with a sacrifice. With Dr. Horrible, though, we have the high cost, but Joss makes it very clear that this isn't a happy ending because of that cost. And I thought that was a nice touch, even though a lot of people seem to be feeling personally betrayed by it.