"The House" from The Doctor's Wife was originally going to be The Great Intelligence too and there was nothing said onscreen to say he wasn't.
Could it be that after escaping from it's bubble universe it has set in motion a means to replenish it's supply of now extinct Tardises?
There are still lots of unanswered questions about the pseudo-Tardis seen in The Lodger and in the hands of the Silence in Day Of The Moon and indeed who blew up the Tardis in the The Big Bang, so maybe the Matt Smith big bad has been the daddy of the Yeti all along.
This second half is quite strong on old school aliens.
The Great Intelligence, The Ice Warriors, The Cybermen, a Silurian and a Sontaran.