I'm betting that the gag with Strax and the memory worm and the Doctor seeming not to fully remember the Great Intelligence were pieces of foreshadowing. Like Strax, the Doctor could be using a memory worm or some other technique to gradually erase his early memories and not even know he's doing it.
I think that's reading too much into the Doctor's memory lapse about the GI. Remember, most viewers of the new series aren't familiar with the old series, and the new episodes have to be made to stand on their own. Having the Doctor remember the details of his previous encounters with the Great Intelligence and explain them to somebody would've been too much of a distraction from the current story, so it had to be kept an Easter egg, a passing reference that would mean something to the old-school fans but not distract or confuse the modern viewers.
In-universe, the Doctor is supposed to be over eleven hundred years old now, and was less than 450 when he encountered the Intelligence. How well do you remember things from nearly 2/3 of your lifetime ago? Even with a lifetime far shorter than the Doctor's?