The Mother says, "What kind of mother would miss her own daughter's wedding?" It only really makes sense for Ted to get choked-up there if he realizes that she is going to miss their own daughter's wedding. IIRC, that scene between Ted and The Mother took place in 2026, four years before Ted is telling his story, so their daughter would have been about 12 years-old at the time. If The Mother has been given less than five years to live, she won't live long enough to attend their daughter's wedding.
My off-the-wall prediction is that the Mother was dying (and had just been diagnosed when that episode took place), but ended up being saved by an organ donation from Barney (or maybe Robin). That's why Ted's story has been so much about before his meeting the mother, and he's letting the kids know how important Barney and Robin were in his life.
Either that, or the mother has been dead for a few years, Barney is dead too, and Ted is going to marry Robin.
Or, for a truly off-the-wall prediction: They're going to pull a Fight Club ending on us, and Barney truly was "legendary" (even his initials are BS), and it turns out that all the "Barney" stories Ted has been telling were about himself when he was a crazy womanizer and Robin ended up leaving him at the altar. At the depths of his despair, he met The Mother and became a whole new "Ted".
The creators have claimed that the finale effectively wraps up the story they started telling in the first episode. In the first episode, the kids act bored when Ted sits them down, and the son asks if they're being punished when Ted tells them he's going to tell them the story of how he met their mother. That doesn't seem like the reaction of a couple of kids whose mother has recently died.
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