Lol, I love this conversation <3 I find the concept of the clothes morphing themselves into something suitable for war, or really just for convenience, I have to agree that the need seems a little silly. I'd rather just go around bare butt than have to deal with the whole thing.
One option that may not have been explored is to make the clothing itself part of the shifter. For example, in the game PROTOTYPE Alex Mercer's jacket, pants, even shoes, are all as much a part of him as his nose or fingers, they just happen to look like clothing. Or, you could go a similar method and have the character essentially be wearing another shapeshifter.
Usually that happens as a result of cheapness on the part of the animators, not directly as the result of a plot device. Transformations in video games usually involve clothing melding into the form because the clothes have been painted onto the model itself. It's yet another one of those plot anomalies that they always hope nobody will ever care to notice.
Have to get this out of the way before I begin on the rest though. In the plot of Prototype, we don't mean for the sake of convenience, his clothes came back when he shifted. He wasn't human anymore, his body, his mind had been over run by an evolutionary-based disease. We don't mean his clothes just came back when he turned back to his human-born face. His clothes, shoes, everything, we
literally a part of his body. The reason for them looking like clothes to begin with was because it was in fact a need for the evolutionary pull that started the whole thing. They didn't even look like the clothes he was wearing when he was contaminated and changed, or any he wore after wards. If you look while playing the game, when he changes his body to things like the blade arm, or the mass bulk etc., the jacket he has melds into the tool, because the jacket is as much a part of his body as his arm is, so on and so forth. Not to say the whole thing doesn't have a crap load of anomalies anyway (like how they don't notice you can fly and climb walls, just because you're disguised as a marine. "It's okay, he's from the government. They can do that") (Die hard prototype fan here, sorry ^_^;;)
But on the "There Will Be No Darkness" concept, I think if the clothes did change, this would be the most credible way of doing it. But then again, this means that if they were naked, then they would always have fur the color of their skin tone. Lol, what if you had a sun burn? "Swear to god officer, I saw him! He was huge, and hairy, almost looked like a dog, but just so damned big! Oh, and he was red as a lobster too! Wait, where are you going? You got to believe me!"
The whole concept of clothing is a tricky one, but for books, I don't really see why people insist on making it a gray area. I think people just don't like the idea of writing out the fact that the person is naked. I know as a writer(some of my stories are of lycans), while I do try to keep it real, and yes, I require my fuzzies to strip or deal with torn clothes, I've always felt awkward. Maybe some people just don't like having to deal with it, and so create that little plot hole. I can understand how it would get sticky for movies though. I mean, who wants to have to make their movie R, just because they show a guy once without a shirt on? In that situation, I think Van Helsing got it right (perhaps that's all they got right. Clouds can deflect the power of the moon, but a bloody brick wall can't? Really?). The clothes were torn, yes, but not so much that they were pulled off of him. When he changed back, his shirt was hanging around his waste in tatters, and his pants were now Urban Decay-esque short shorts.