1. Necromancers arrive as invaders (in a siege) as often as I've seen them, and can even be pretty stealthy! I didn't see them until they were almost on top of my fortress. They come with their own zombie armies, and will animate any dead stuff nearby. For me this has been more or less dead wildlife I've failed to clean up, refuse from butchering stuff, and the victims of their armies that didn't get inside fast enough. Line of sight is needed, but that means they can cast across Z-levels. I had a serpent woman necromancer who was animating things from the bottom of a pond, she could see up the Z-levels to her targets.
2. Vampires are created in world gen when somebody angers a god by profaning a temple. Those vampires can then infect other people to vampirism when they fight. Vampires can emigrate to your fortress as migrants in disguise, claiming to be somebody else. They very much can die, but they're very hardy and tough in battle. As for what to do with them, that's your choice. The Justice system will help you figure out who's a vampire if there are witnesses to their killing, but you don't have to do anything. You could even lock them up and have them be part of an all vampire military that gets set loose to kill invaders. Vampire citizen obey burrows, so it's easy to keep them away from other citizens if you want.
3. Were-Creatures are originally created same as vampires, and their victims if they live often also become the same kind of were-creature. A Migrant can be one, but the only ones I've seen so far were elves who wandered onto my fortress in their creature form, attacked something and ran away. I believe a full moon is once a month, so that's how often you'll get your crazed murdering machines. Keep in mind were-creatures of the same species are friendly when changed, and your dwarves won't blame a were-creature who changes back for his beast-self's crimes, so were-creatures can be useful too.
There are a few bug fixes, for example traders now come with wagons, so the path to your Depot must be at least three squares wide, no staircases.
Plenty of new creatures, including a few birds, Keats, Eagles, Raven to name a few, a few new land animals including wolverines, porcupines, and many many more (mosquitoes), including the giant and people versions of all the new donation creatures.
In addition to evil rain in areas, which causes minor sicknesses and is gross (slime, muck, blood), there's clouds of more deadly gases that can float through your areas (also only in evil areas).