Since you are normally so convincing, I have to ask: how can Rory and Amy beat out Donna and Rose? The two of them are less characters than they are cardboard cut-outs, despite the best efforts of both actors to give them flesh. They have no real connections to family or friends. They have no lives independent of the Doctor. Their personalities fluctuate as the plot demands. Without Amy, I'm not even sure "Rory" as a construct could exist. The companions had been so interesting, until them!
I like Amy because her time with the Doctor has really been her life story. She met him as a little girl, kept him alive in her imagination for years, and then took her place alongside him in his adventures through space and time. I don't call that being a cardboard cut-out, either! On the contrary, I'm fascinated by the way her life intertwines with the Doctor's. The Doctor has called other companions his best friend -- notably Donna and Sarah Jane -- but Amy's story is the first time I felt that the program really showed us that instead of just telling us. In my opinion, it makes a lot more sense to call Amy and Eleven best friends than Ten and Donna or Three/Four and Sarah Jane. Just having a lot of adventures together doesn't equal best friend status, in my book.
As for Rory... Rory is my idol, seriously. Rory Williams-Pond wins me over in a way that I think Russell T. Davies was attempting with Mickey but just never managed to pull off. That character, of the primary companion’s love interest, is realized beautifully in Rory. It’s clear, especially in Season 6, that he likes traveling and having adventures with the Doctor too, but he is mainly there because of his lady friend. His life is as connected to Amy as hers is to the Doctor.
But that’s not a bad thing! On the contrary, Rory is the ultimate romantic. He has proven, time and again, that he is completely devoted to Amy. He will give up anything, with no complaint, to be with her. The lifestyle has definitely grown on him, but he was willing to travel in the TARDIS even when he felt resistant to the Doctor, because that’s where Amy wanted to be. And of course, he doesn’t hesitate at all before volunteering to spend 2000 years guarding her inside the Pandorica. From what we see, he never even questions that decision or offers a single complaint about it. He is a rockbed of dedication to his wife, and he will wait patiently for her for millennia or lead armies across the universe to rescue her and their child. Now that’s love!
It's a shame you don't feel the same way, but I find the Doctor-Amy-Rory dynamic fascinating. It's great to see the way their respective loyalties pull them. They're all friends, but each one feels very differently about each of the other two. (Amy views the Doctor and Rory differently, Rory views Amy and the Doctor differently, and the Doctor at least arguably views Amy and Rory differently.) I think some of the best moments of the current Team TARDIS have been between Rory and the Doctor when they're forced to confront the different ways they feel about Amy.
