As far as social rejection, somewhere in-between would be good. In Morrowind it was kind of obnoxious that glowing eyes made you a universal pariah no matter how covered up they were, and it was equally obnoxious in Oblivion when basically no one cared. Supposedly Cyrodiilic vampires could blend in, but tell that to the notorious ugly-old-man-face. Even at the worst stage all you got was the occasional nasty remark. A way to hide your condition, and a less universal reaction that could let you wear a different disguise or go somewhere else, would be nice. Also good would be if the AI were advanced enough for layered reputations and recognition; if you're discovered in a town where nobody knows or recognizes you, word doesn't spread to areas where you're popular. If no one in Town A has heard of Jim Jones, how are they telling everyone in Town B that this vampire they spotted is Jim Jones? Suspicion would also be a cool addition, such as guards searching you for weapons when approaching royalty or wanting to see your face in town if it's shrouded, and they're actively looking for someone (wanted posters). I would enjoy hiding out in poor sectors riddled with plague, where nobody looks for long, where people covering themselves against the cold or to hide their own diseases is common, where I don't have to worry about catching anything myself thanks to the vampirism or worry about guards particularly caring about the dead homeless. I could sleep anonymously in a poorhouse during the day and slip out without questions during the night to hunt.
As for feeling different, you could try giving a werewolf bonuses to things like climbing (if implemented) and bashing damage to objects, in addition to any strength-based boosts. Dismemberment, in reality, is not easy or common, and it shouldn't be in combat (again, if implemented), but with claws and superhuman strength would probably not be so hard to lycanthropes. Imagine a werewolf rapidly scaling the town wall, ripping out the door to a house, and tearing the occupant's arms off as they raise them in self-defense. That is a beast you don't want to screw with. Instead of the "one kill per night" limit, you could have something similar to the breath bar/suffocation effect, where the meter ticks down the longer you go without spilling blood and starts to harm you if ignored. Not nearly as quickly, of course, but it would help add some aggression to the form and make it feel more like playing a frenzied monster.
And of course, downsides. Vampire and werewolf hunters, for example. Professionals, who are an actual threat to ME, and not just more cannon fodder with a different equipment setup. A danger of losing equipment during a werewolf transformation, instead of it all sticking in my fur or something like Bloodmoon. Vampires needing sleep during the day, and the sun being a deadly threat at all times (immunity in Oblivion made me cringe).
Well thought out post. Becoming a were needs to become an alter ego or another being altogether. It can't be your