It took half the book, but I think I've finally put my finger on why I struggle to follow the plot of Souldancer. It all hinges on the motivations of the primary actors.
Say what you will about George Rape Rape Martin's Ice and Fire Omnibus, all of the characters have easy to follow motivations. Team Evil wants the Iron Throne and will do anything to hold it. Team Not Quite as Evil wants the same. Team Chump wants to keep their family safe from the machinations of Team Evil. Team Blonde wants her throne back, but needs to run around not-North-Africa gaining enough XP to earn enough gold for an army of henchmen and a dragon mount. This makes it easy for the reader to constantly gauge the relative positions of the actors.
In Niemeier's other works - okay, the only other one I've read so far is Elegy for the Locust, his short story in Forbidden Thoughts - the protagonist is motivated by a desire to usurp his master. He seeks out the dark arts, and succeeds beyond his wildest nightmares.
Most of the protagonists and antagonists in Souldancer have motivations that are vague or hard to track. Xander, thrust out of his tribe, is a wanderer who falls in with a group of adventurers. Those adventurers want to look ruins for old tech, and its only later that we realize Thurif's real motive was to secure enough power to become death, destroyer of gods. At the tail end of the dirty thirties we meet Gil and the crew of the broken down Serapis, who get shanghaied when Asltin and company bring Zan aboard. Their sole motivation from that point on is staying alive - they are caught between the pirates and their former master who would have them killed for their failures. But that leaves them as just more leafs-in-the-wind.
As another example, our adventuring party on the run from the bad guys, so they need a ship. They get one, but that's a tertiary step. I don't know what the plan is for after they have the ship. It quickly becomes moot because once they have the ship they need to escape from pursuit, and an epic space battle occurs. But if Zan gets away, that just means he can pick up his friends so they can...still not sure what the ultimate goal is here.
The antagonists are hard to track as well. The Lawbringers work for Shaiel's Blade and Shaiel's Will, who obviously work for Shaiel, but work toward what? The factions are clear. The conflict is clear. But it's never clear how close anyone is to achieving their goal.
Which can be fine - a roller coaster ride featuring a character bouncing through the pinball machine of life at the mercy of fate's bumpers can be a lot of fun. It's how I've had to read this book, not thinking or anticipating, but just letting the plot wash over me and occasionally making connections that don't have any real meaning since they don't have any more bearing on the future than anything else in the book. The stopper in this case is that there are so many different factions working with and betraying each other for short term gain, that I just can't follow the ultimate why of the book.
Other than survival. Staying alive is always a priority, but there must be more to the Middle Stratum than this.