He doesn't like that she flirts.
He doesn't know why, not for ages. He just knows that it harrows some part of him very deep down, like an unexpected shiver. She lowers her voice and her eyes at French painters, brushes up against the arms of Jephany warlords, giggles at a Thelmish curator's bad joke, and something in the Doctor's chest twists, and everything sounds…out of tune, for hours afterward.
He tries to tell her once. He takes her aside after she's chatted up one too many historical figures and says it's really a bad idea, it complicates things, there are social norms she may not be aware of or messages she may not realize she's sending, and would she please just learn to control herself and not jeopardize…things?
And of course, Amy Pond smiles, and she leans in, and she says something in a sweet, teasing voice, something inconsequential and delicious, and flounces away. He stands there lightheaded, and hates himself for it.
He doesn't like that she has no sense of boundaries.
After the Dream Lord she finds him, curled up in the library, and she wants to talk. He would run, but she sits on him, crushing his book and pinning him against the armchair with her eyes. She wants to know the answer to her question, whether he believes the sour, heavy words that she heard the Dream Lord speak, whether he listens to the frightening music that drifts up from the oldest parts of his soul. He tries to deflect her, but she will not be deflected. In the end, he shouts at her, venom and steel, and there is a horrible, horrible moment before she stands up and walks out of the room. He covers his face with his hands and does not move for hours.
He doesn't know when she finds the time to hide the note in his book–she must have thought he'd come back to read it soon, but he doesn't, not for years, not until long after he's lost her. He finds it by accident while re-alphabetizing the library: a little white index card with faded letters, her handwriting.
I'm sorry, I should've shut up. Gotcha. Amy x o.
He sobs alone in the library. The card wears out over the years until he has to throw it away.
He doesn't like her singing voice.
It's a low voice, a strained voice–she puts too much effort into it, trying to sound like a rock star, probably shredding her vocal cords–and she doesn't give a damn about staying on key, stumbling in and out of melodies as she does, and it drives him mad, especially when he knows how the song goes and she won't let him correct her. There's one time after a particularly gruesome Beatles concert when she's just a little bit drunk and is absolutely butchering "I Wanna Hold Your Hand" in circles around the TARDIS console, and when he finally can't take it anymore, he is about to jump up from his chair and intercept her, probably with a very sensitive piece of constructive criticism, although he can't entirely rule out the possibility of just grabbing her by the shoulders and screaming SHUT UP!
But Rory catches his eye and shakes his head. They enjoy a brief moment of shared longsuffering before Amy pounces on her husband and pulls him after her towards their bedroom. The Doctor closes his eyes and relishes the silence.
It doesn't last long, though–not for him. He has Amy's voice stuck in his head for the next week and a half, singing "I Wanna Hold Your Hand" at the top of her lungs.
He wishes she did.
He doesn't like her aunt.
Sharon Bailey has sharp eyes and a subtle mind, and when they pay Amy's family a surprise New Year's visit, she sits quietly on the couch and just watches them. Amy and Rory are too giddy to notice, laughing with Amy's parents, trying to explain the TARDIS and summarize months of adventures, and Mr. and Mrs. Pond don't notice, either, pressing champagne on the Doctor and asking for stories and making jokes about time travel and "bigger on the inside" and thanking him for keeping their daughter and son-in-law in one piece so far. He likes Amy's parents. They're as bright and bouncy as she is, and they don't make fun of his dancing.
But Aunt Sharon watches him, and around eleven o'clock she pulls him into the kitchen, away from the party, and points a spoon at him. "Don't even think about it," she commands.
Backed up against the refrigerator, staring at an older, crosser, much eviler version of Amy Pond, the Doctor swallows and very politely asks, "What?"
He closes his mouth.
Aunt Sharon steps forward. "You fucked up her entire life, all the way back to when she was seven." She glares at him. "Don't you dare fuck up her marriage."
She leaves him there, and he's so tired. A few minutes before midnight he slips back out to the TARDIS so he doesn't have to watch.
He doesn't like that she's not from Gallifrey.
Because if she was–if she was one of his people, his species, if she was looking forward to centuries of breathing, running, laughing, centuries of new bodies, new faces, all of them ginger (how could Amy Pond ever be anything but ginger?)–if he could put his two hands against her chest and feel two hearts racing beneath his palms, look into her eyes and see the same spinning, burning history that spins and burns in his own memory, hold onto her waist in the dark and call her by a new name, a name that only he will ever know, he and no one else in the universe, in all the time that ever was…
These are the dreams that he wakes up breathless from, the reasons why he can't always look at her, meet her gaze when she's talking. Her eyes are almost empty, just filled with twenty years, a breath. A flirtation with time.
He hates her for making him dream.