My take on the direction of Era 2:
First, the books were initially unplanned. From my understanding, Brandon wrote AoL as a side project, originally intending it to stand alone as a single novel - of course, that didn't happen. Instead, we now get this follow up trilogy. I am convinced this is because Brandon knew he had some great characters to work with and found a really interesting way to use these characters to reveal important aspects of the Cosmere to us.
This idea is supported by the fact that important Cosmere characters are showing up at key moments. I've been away from the forums for a while, but I would assume everyone thinks Marsh is the inquisitor that gives the book to Marasi at the end of AoL? Harmony is clearly very concerned about Trell and has been open and honest with the Kandra about the threat he/she/it posses: that is to say, they have no idea what it is attempting to accomplish. The Kandra are back - though they were never really gone - and making themselves known to important characters. Hoid makes an appearance in SoS, driving Wax's carriage. I'm sure there are other cameos that I am missing, but the fact that Wax and Marasi are both learning so much about Harmony and how shards work, I have a very strong feeling some big Cosmere reveals are coming in these books.
As to a narrative direction, I think that Wax may pull a "Dark Knight" imitation in this next book. He is depressed, sad, and very confused/mad with Harmony, and he really isn't what Elendel needs right now (at least in my eyes). I think he will still be a big part of the book, but I think he heads out to the roughs again (perhaps bringing Steris with him), leaving Aradel and Marasi to take care of the city. I think Wax leaves due to a clue about the origins of the Set and it leads him out of the city (perhaps something about the Lost Metal being linked to the Bands of Mourning?) Also, what are the Bands of Mourning? They were specifically mentioned in SoS. Anyone know?
Anyway, Wayne is very much a wildcard here... I don't know if he leaves with Wax or stays in the city to continue meeting with the girl. If he does the latter, I think he makes some sort of progress with her. Not sure what that would lead to, but could be another event that Harmony is directly influencing. We will see.
I think the Set nearly overwhelm Aradel and Marasi while Wax is away. I also think they fight back with the help of Hoid or another worldhopper and/or Marsh. I REALLY want to see Marsh show up and just dismantle people. Heck, lets have him fight Wax. Not kill him, but just kick his butt, reminding him that Harmony's plan is far more important than Wax's personal comfort. If there is any character that would known the worth and pain of self-sacrifice for the greater good, I can think of none better than Marsh. I mean, maybe Kelsier, but... I'd rather see Marsh.
Eventually, Wax realizes the world doesn't revolve around him (because let's face it, he totally thinks this right now), and makes a decision that his uncle never saw coming. This actions leads to the revelation that the Set is working for Trell. (which I think a lot of people already suspect). This gives Marsh/Hoid/other worldhopper and Harmony enough information to slow Trell's attempts to utilize the Lost Metal to gain control of Harmony himself. This realization is the huge Cosmere bomb that gets dropped on our heads sometime during the last book. We suddenly figure out that shards themselves can be controlled through Hemalurgy. In some ways, I think this is hinted at in the appendix of SoS. The writer of that breakdown of the magic systems of Scadrial is extremely interested in hemalurgy, and i think there is a very good reason for that.
At the end of the first MB trilogy, we had a character gain control of two shards. We really haven't had such a huge Cosmere altering event since then. I have a feeling we're about to get another.
Hopefully all that makes sense. It sounds rather interesting to me... What do you all think?