Poirer got him down once but couldnt really do much to him, I think a bigger issue in that round was actually that Conor couldnt break away from the clinch. I'm guessing that was Dustin's aim, to sap his cardio.
I'd agree size is a massive issue, Conor's countering style was much more effective when he had a massive reach advantage forcing opponents to push in although I think with Dustin you see more a tactical difference in the two fights as well as improvement. In the rematch he knew that staying at range wasnt a death sentence, that he could take Conors shots provided he didnt get caught off balance.
The Nate fights for Conor were a bit like the Cain fights for JDS IMHO, they showed how he could be beaten, the difference being Jnr's sheer toughness allowed him to carry on having sucess for awhile.