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Warren Frey — that shill for SPACE* — had some interesting recent thoughts about why a non-platonic Doctor worked in Series 1-4, along with a request that Moffat not go there in Series 5. While I agree we don't need a big honking love story subplot again, some level of affection between the Eleventh Doctor and Amy Pond may have to be explored….
* Yeah, yeah, Warren does this other thing, too.
Nice thoughts, though I think that by blurring the lines between various sorts of affection you do the issue a little too much justice. After all, the Doctor has always (eventually) felt warmly about his companions, with Jo, Sarah Jane, and Romana II all sharing very strong relationships with the Doctor. (See the great scene in Fenric where it's the Doctor's faith in his past companions that keep the haemavores at bay.) Those dynamics never explicitly crossed that fuzzy line into romance, whereas the Doctor and Rose did–it's as if the Doctor never loved until he met Rose Tyler, which is rather baffling for myriad reasons. We'll see what happens with Amy Pond–Moffat does have a soft spot for romance, so we'll see how he plays with the scenario. Personally, I think it would be brilliant if Amy were a lesbian–not only would it continue NuWho's grounbreaking ways regarding LGBT characters, it would, hopefully moot the point entirely.