I think personal preference plays a big part. For me, I didn't buy Rory as an interesting enough alternative to travelling around in space, therefore perceived Amy as having less of a real choice. Either way, she's attached to a particular person. I think because culturally the happily-ever-after is seen as a female desire, some viewers would view it as sexist; the assumption being that were the character male, they wouldn't have to make that decision. Of course, we don't know whether Moffat would have used the same quandary if it had been a male companion; to me that would have been more interesting.
The blokes in the RTD era aren't really portrayed as a serious alternative to the Doctor; the companion's dilemma was more about family ties. As a culturally universal thing, I found that more identifiable, which seemed to be the thing about the RTD era. Of course the show has moved on and it hasn't needed to provide as much that we can identify with because it has its audience. I think now with its popularity, people expect a bigger scale anyway. But to an extent, the viewer needs to identify with the companion, where in New Who they seem fixed as human. Maybe it was done a bit simplistically by RTD with Rose's working class background and family history, but Moffat's characters seem to lack identifiability. Obviously you're not going to identify with travelling through time to save an alien but the human aspects don't feel as identifiable to me. Because people will superficially latch on to characters which resemble themselves- their sex, race, class, etc.- the portrayal of those characters is going to feel important to them.
What I liked about the TVM was that you had a successful female character with concrete achievements in the human world. She was spirited and had a sense of humour without being a sassy quipster. As such she was much more identifiable; a bit irritating at times maybe but identifiable.
