A/N: This is kind of all over the place an non to coherent, sorry about that. All mistakes are my own.
It's spite that brings River to say what she does to Rory as she his trying to open the locked door in the tunnels beneath a warehouse in Florida. She is mature enough to at least admit it to herself, if nothing else. Not spite towards Rory so much as the Doctor and the situation they have found themselves in. The pain in her voice is real and its masks the bitterness and anger. She can't even bring herself to feel guilty about Rory's despondent reply.
Of course he knows what its like for a girl to grow up knowing the Doctor. And of course he thinks that River is talking about Amy. She's not, though Rory won't understand that for some time. River herself didn't understand it at first, not until recently.
River is moving forward, but to her, the Doctor is moving back. He's merely fascinated by her while she has been in love with him her entire life. She had thought, in the beginning, that he loved her too. When they first met and he swept her off of her feet into a world of adventure, accidentally slipping and speaking snippets of events that were to come. That man had loved her. Her Doctor, he loved her, she had been sure.
Until she met Rory. Not their first meeting, nor their second, but meeting in the middle of nowhere mere hours ago. It was the desperateness in which the Doctor had held Rory, however brief, that clicked everything into place. Amy hadn't noticed, nor had Rory. They didn't know the Doctor like River did, the little things in the way he held himself that told entire stories.
The Doctor at 1100 years old who has recently seen Jim the Fish. River remembers quite well, Jim. She remembers the Doctor whisking her away, as always, but louder than normal as if to cover something else. She remembers his pain and how no matter how hard she had tried, that she had been unable to make it completely disappear; unable to kiss it away.
And now the last piece of the puzzle had slid into place.
He loved this man, the Doctor did. And now, as River thought back to different adventures, planets, dangers, and kisses she realizes that every time the Doctor came to her he looked a little pained. A band aid then, or an ointment to ease the Doctor's pain. That's what River is.
She wonders what had happened between the Doctor and Rory that led him to be as he was the day of Jim the Fish. She wonders how it all works out with Rory and Amy and the Doctor, if the Doctor even ever tells Rory the truth. Probably not, that stubborn man.
900 year old Doctor doesn't love Rory with the fierceness of 1100 year old Doctor. A new spark, River thinks. How many times had the Doctor come to her after visiting Rory? She didn't want to think about it, but she couldn't not.
River hated the Doctor a bit, for the first time with true anger. Not now, he probably hadn't realized yet, but later the Doctor would use her. He would use her after seeing how completely and quite possibly madly in love with him she was. He would come to her and dangle the world in front of her nose, knowing that one day she would find out the truth.
The mission is finished. Its another adventure to pen in her journal as she sits in her cell awaiting the next time. The Doctor is walking away from her, and River is mad. She is so mad at this wonderful, terrible man. But mostly she is mad at herself, because knowing what she does now, she still loves him.
And so when he turns back around she kisses him fiercely.
And when he says that its the first time, she know it will be her last. He'll kiss her countless times more, but she can't do it. The Doctor loves a man who spent two thousand years waiting for the woman who is now his wife. River's only satisfaction is knowing that she isn't the only one who is second best.
As she writes down page after page of new information, she longs for the days when she was young and ignorantly in love. It was better than being aging, in love and bitter.