I don't get the commentary by some that if Emerakul is defeated, it's bad storytelling. In fact, if go so far as to say, given the story to this point, it's actually the right call story wise. Here's my reasoning:
Defeating Emerakul doesn't defang the Eldrazi. The fact is, they were defanged as soon as 2 were killed at once in Oath. Once that happened, there was no way the third Titan would be seen as a legit threat, even with all the build they've done. And even if Emmy were to win here and make two new Titans, the fact is that the new Titans would be jokes, since it was clear that Emrakul was so much more powerful than the other two titans that no other force on their level is worth considering. Effectively, a win here only helps Emerakul. It makes her minions/allies look weak, and it makes the Gatewatch look bad, since their first win retroactively was only defeating a few henchmen, since Emerakul was so clearly the true power.
As soon as Oath happened, there was only one way to logically take the Eldrazi. They were the starter villains, who appeared insurmountable in order to require the team up, but to still be defeated cleanly, making the heroes look strong. Compare to Trigon in the 80s Teen Titans series or Nightmare Moon in My Little Pony.
So, if that's the plan, what role does Emmy play? I think she is here for two reasons. First, as implied by MaRo, she establishes the new level of storyline continuity, by having a major plot point of the previous block affect the next, you teach the audience to care about blocks together, and not to just forget everything, as was largely the case before. Second, it establishes the status quo. This is that episode right after the series premiere (see "the Train Job" from Firefly or the "Zabuza"arc of Naruto). It's about showing the recurring beats the audience can expect which makes the changes and breaks easier to take in. In this case, Emerakul serves perfectly as a villain that doesn't need to be built up due to the previous arc, so the story can focus more on the actions of the heroes. I imagine going forward the story structure here will be the rough template for future blocks (about half focused on world building, and half on the Gatewatcher of the week in the first Set, we'll see what the format is for the second set)
Hopefully that made sense. At least it did in my head. Sorry about using some more obscure references, but hopefully there is at least one you recognize in each case.
On an unrelated note, there was one element of this week's story that scares me more than anything Innistrad or Emerakul could possibly come up with:
Please, please, PLEASE, PLEASE PLEASE PLEASE PLEASEPLEASEPLEASEPLEASE do not introduce a Jace/Chandra/Lilliana love triangle. I genuinely feel that would be the worst possible thing to come out of this, and would greatly threaten my likelihood to keep up with the story.
That being said, I'm about 70/30 that Lili joins the Gatewatch, and establishes herself as the snarky antihero of the team.