I don't remember his having companions who came and went during their tenure on the TARDIS, but to be honest, it's quite a while since I've watched much Classic Who. I remember the Doctor's companions travelling with him all the time for however long they were with him. In hindsight, the vision of Amy and Rory comfortably ensconced in their married life with the Doctor having to send them cryptic messages seems rather at odds with the pair of them rushing into the TARDIS at the end of S5 still in their wedding gear.

As far as the nookie goes, it seems to me that River and Eleven are getting flirtier with each meeting, to the extent that I'm thinking that surely something's going on off screen by now ;-)

I don't think the episode fell short as such - but it certainly asked a lot of questions. it's a two-parter though, so that's to be expected, even if it is incredibly frustrating!