I actually never found Tobias that annoying. Yeah, he talked about being a bird a lot, but for the most part he had actually accepted it. I mean, okay, in book 3 he whined a LOT about it, but it was still new to him, thus completely understandable.
I actually found that Marco bringing up his mum so much in the first 5 books was more annoying... I mean, he had two years to get over it, and he still hadn't. (Once he found out she was Visser One, it's fine though, because I think ANYONE would be upset about that) But before that? *shrugs* I mean, I know loosing a parent is hard; I've been there. But 2 years later, he should have at least moved on enough to not have his voice break every time he mentions her.
And while we're talking about characters not moving on, how about Jake's constant "I have to get Tom back!" thing? Or Cassie's constant moral battles? Ax missing home? Rachel's being in love with a bird-boy?
I guess what I'm saying is that every character has something to whine about, and they all do plenty of whining. They're teenagers with the world on their shoulders and emotional baggage. Whining is almost a requirement.