Well, to be fair, she does rub her specialness in the Doctor's and the audiences face. She's fairly Mary Sue-ish, in that she's a new character who has special skills and special knowledge that most guest stars on Doctor Who don't have, particularly in the area of the Doctor himself. And to the extent that she obviously delights in making him feel a bit uncomfortable about it and enjoys knowing things he and others don't know, it can come off as smug.

Now me, I'm not bothered, because Alex Kingston can do no wrong in my eyes and I feel some of the best people to surround The Doctor with are people who aren't awed by him and who can match him for mysteriousness and cleverness and pulling surprises out of their ass-ed-ness, which is why I liked Romana, and why I liked Captain Jack as a companion much more than Captain Jack as Torchwood leader. But it's not so much that she's confident as she's clearly being written as mysteriously special. Of course she'd have to be if she truly is (The Doctor from the future/The TARDIS from the future/The Doctor's wife/The Doctor's daughter/Rassilon/Whoever). And again, Alex Kingston. If she kicked a puppy the puppy was probably a real asshole.