Just wanted to add: The argument about 'how many lives were saved because they are werewolves' just doesn't wash. The Companions weren't always werewolves. And there isn't a single mission for the Companions that requires anything more than good old fashioned steel.
Having a good blade doesn't make you invincible. And although a werewolf isn't invincible either, it does give them a greater edge when used tactfully (hence why they made a pact with the Glenmoril Witches for control of it, as an out-of-control werewolf wouldn't be that useful).
No, no one other than the Circle (and probably the maid) knows about the wolfishness - that's stated outright by the Circle themselves. And with all the flunkies always hanging around, there's plenty of MANpower for anything the Companions would be hired for. And if noone but the Circle knows, then no one is going to hire the Companions for a job only werewolves could accomplish.
I don't mean for jobs that only a werewolf can accomplish, but a job in which being a werewolf gives a greater chance of success. Like, would clearing out an abandoned fort full of bandits be better handled with 3 or 4 warriors (like the bandits are used to fighting), or a pack of hungry werewolves designed for hunting people (that the bandits wouldn't expect and be freaked out by)? Sure, a group of warriors could possibly handle it, but there's also more of a chance for losses or serious injuries.
Additionally, Aela and Skjor both love their wolfishness so much, they are willing to give up an afterlife with humans for one with animals. I'd say they'd gone wolf. Their attitudes actually remind me alot of the folks making werewolf-enhancement mods - I WANT MORE POWAHH!!! Everyone seems to be totally ignoring the fact that Skyrim werewolves are not some cool clique from a teen movie - they are men and mer who have been horribly transformed by disease into creatures without conscience or control, who are greatly feared and shunned. Especially to the super-superstitious Nords!
Werewolves are supposed to be powerful. The reason for the werewolf-enhancement mods are because werewolves are poorly balanced at higher levels (like a lot of things in the game *cough*Destruction*cough*). No, they're not "cool" to the people of Skyrim, and they are feared and shunned by most... no one really suggests otherwise. The Circle has a unique position on it, though, because they don't suffer from forced transformations and they don't have to kill to survive, unlike the ones like Sinding.
That the Companions have learned how to control it makes no difference. It actually makes it worse. They consciously infect themselves with something that REQUIRES them to feed on their own kind. Saying it's not cannibalism is like - well crap, it IS cannibalism, no matter how you slice it. Werewolves are NOT a new species, they are all still men or mer. If they weren't, they couldn't be cured!
Just to pick a nit, the first werewolves are technically daedra. They were created by a Daedric Prince of his own essence, like Dremora, Scamps, and Golden Saints. A person in beast form normally loses all control to the will of a beast, meaning it's no longer the person they originally were, so it's not so clear cut what someone in beast form actually is (i.e. a person with a mutated body, or a daedric creature temporarily possessing a person's body).
While I agree that playing as a werewolf needs revamping, I am damn glad someone is taking he Silver Hand in hand, because all these "be-a-werewolf-as-long-as-you-want-with-turbo-power-too!" mods are really getting on my nerves. I have yet to see a werewolf mod that is not going to make the PC so OP he'll cakewalk on master. To each his own, I suppose. Some folks play the game only for the car crashes.
Balance is a difficult thing to achieve when so much is unbalanced. A big complaint I've seen with werewolves, next to how there's so little downsides to being one, is that it's useless to be one at high levels. But without the CK and a large-scale re-balancing of everything, you can't really do much except make them stronger in simplistic ways. The werewolf mods out now are pretty much the extent of what can be done now to fix them without the CK, while mods like this, or the aforementioned Call of Hircine, are much more long-term projects that are waiting on improved tools.