Ordinarily I would've agreed that Fuller was simply referencing the first quote above (about coming to an end), simply because, as many have said, 'All good things come to those who wait' really isn't the saying at all.
However, since so many people seem so convinced of the idea, I got curious and did a bit of googling. Lo and behold, regardless of what anyone thinks of the validity of the 'saying', Bryan Fuller apparently does subscribe to it, based on this interview:
http://horrornews.net/104176/interview-bryan-fuller-hannibal-2/
The relevant quote:
Now what would you say to the fans right now because so many people love the show.
Bryan Fuller: I would say, “all good things to those who wait.”
I think Hannibal would say the same thing.
Bryan Fuller: (laughs) It seems like something Hannibal would say.
So that puts a rather more hopeful spin on things...