I so am not qualified to be writing in this fandom yet.
Spoilers up through Amy's Choice.
The Doctor doesn't dream of Amy Pond.
He doesn't dream at all. Time Lords don't dream. His sleep is an endless dark expanse of time, a pool of infinite inky depths into which he sinks and floats until poof, he simply wakes. He has no regrets about having no dreams. There are too many things, too many ingredients for nightmares in his past. The Doctor would rather not dream.
So The Doctor does not dream of Amy Pond.
There is no fantasy version of Amy to haunt his sleep; no Amy who chooses The Doctor over Rory, who looks at him as her red, red hair whips across her cheeks and says You are mine and I am yours and we will never be apart.
There is no Amy who traces a finger across the bones of his brow like she's trying to memorize him, who touches the curve of her lips softly to his, with love and desire rather than lust. Who breathes a new kind of life into him.
The Doctor doesn't dream of this because he dreams of nothing at all. The only Amy he has is mad, mad impossible Amy Pond, with four psychiatrists behind her and a silent crack in her bedroom wall that follows her wherever she goes. Amy who kisses him up against the Tardis, pulls at his clothes and teases him and chooses Rory.
Perhaps, he thinks, it would be better if he could dream these things. Then he might know what it is that he wants from Amy.
But The Doctor doesn't dream, and Amy's choice has come and gone. The Amy he has is one who loves Rory and is getting married whenever tomorrow comes. And that's good. The Doctor is pleased about that. He'll take that Amy and be happy about it.
Because without her; without Amy Pond (who will leave him one day), well then who does The Doctor have at all?