I think @Madeyedexter's comment hits the nail on the head. This sounds like the Women of the Otherworld series, later retitled to Otherworld by Kelley Armstrong.
The series starts with Bitten. Elena Michaels is the partner of the Alpha's adopted son rather than the Alpha's daughter, but that's primarily because werewolves do not have daughters. The only way to get a female werewolf is for a woman to survive a werewolf bite. This is rare, and Elena is the only female werewolf in the world.
Elena Michaels is the world’s only female werewolf. And she’s tired of it. Tired of a life spent hiding and protecting, a life where her most important job is hunting down rogue werewolves. Tired of a world that not only accepts the worst in her–her temper, her violence–but requires it. Worst of all, she realizes she’s growing content with that life, with being that person.
So she left the Pack and returned to Toronto where she’s trying to live as a human. When the Pack leader calls asking for her help fighting a sudden uprising, she only agrees because she owes him. Once this is over, she’ll be squared with the Pack and free to live life as a human. Which is what she wants. Really.
The on again off again relationship is mostly in the backstory. And it's off at the point where Bitten starts. As can be seen in the blurb above. The relationship becomes pretty much on, with mild drama, following the events of the first book. The uncle/brother's friend relationships don't match though.
Elena is being groomed for Pack leadership by the current alpha Jeremy, although it takes nearly 10 books to actually come to something.
There aren't any bird shifters in the series, but Frostbitten, book 10, includes an race of potentially Neanderthal, wolf/bear shifters. The whole thing isn't really very clear, but they're big and more bear-like than wolf-like without being a full animal change like the werewolves are.
