1. GOP had a consistent polling advantage on voter engagement, even going as far back as August. The Romney campaign placed a lot of stock on this. (see here: http://www.politico.com/news/stories/0812/79665.html) The polls might break for Obama, but the Romney campaign was banking on something else...
2. Polls attempt to account for the simple error that people are more likely to say that they'll vote than will actually vote. (see here: http://www.gallup.com/poll/111268/how-gallups-likely-voter-m...) The Romney campaign was predicated on the idea that GOP voters were likely to get out and vote, while Obama voters would say they were going to vote but then drop out on Election Day. That is a polling blind side that Nate Silver couldn't account for.
The Romney campaign didn't accurately test their engagement assertion. They relied on journalist polling, but engagement didn't turn into votes. The Obama campaign did the opposite: they targeted voters who might be disengaged and directly went after those with their GOTV efforts.
There is a HUGE debate that always goes on around election time with politicos around who matters more. Is it more important to try to sway independents (i.e., go after the middle), or is it more important to fire up your base? Romney won independents but Obama got the base turnout, indicating that a GOTV effort targeted at the base might have worked, had it been used effectively. (see here: http://abcnews.go.com/Politics/OTUS/exit-polls-obama-loses-i...)