I really enjoyed the book, especially the new space-related powers and enhancements, and the Doyen.
The one thing that Just Bugged Me from the original Trinity Setting, and which stands out even more with Nexus and A Breed Apart, is the nova Fermi Paradox.
A Breed Apart discussed the potential for very fast exponential reproduction of novas, with reproduction-oriented powers enabling 10x or greater annual growth, with trillions of novas in a decade. In the early Nova Age one could explain the failure of this to happen as there being insufficient time for many such novas to arise, and ultra-powerful novas actively neutralizing them. But by the time of Trinity it becomes harder to explain why some inhabitants of the aberrant colonies haven't done this, given that we are told they have intensive breeding programs to face off with the low-Taint novas. Perhaps that is still seen as too dangerous by leaders like the Colony (who might not be able to control fast-spawning novas), or would constitute the ultimate WMD and bring about a Final War with the rest of the novas.
Even without ultra-rapid breeding, nova populations would still be growing exponentially, albeit with a doubling time of decades instead of months. Since they are capable of interstellar (and intergalactic, for some novas of observed power levels) travel and colonization, that would fill the galaxy within a few centuries, and all the billions of visible galaxies a few centuries after that. They could then create or assimilate other universes, expanding their multiversal empire by billions of times every centuries. Even if expansionist nova cultures only happen once in 10^1000 universes, they should already have assimilated everything billions of years ago (and we are told the Doyen have been around for billions of years).
Nexus says that the emergence of novas is incredibly rare, happening only once in our galaxy, perhaps even only once in our universe, but any meaningful frequency is hard to make stable.
For non-nova cultures, Nexus reduces the problem by having the Coalition and Doyen act to suppress advanced technological civilization in the Milky Way for billions of years. But the fact that many intelligent species emerged in the Milky Way indicates the other galaxies should be populated, and intergalactic travel is quick and easy with high technology levels in the Nexus tech level system. So out of the hundreds of billions of species that would have emerged in the visible galaxies based on Milky Way development rates, why haven't some become technically advanced intergalactic or interdimensional expansionists crushed the Doyen billions of years ago?
The easiest explanation in-setting would seem to be that the Milky Way and our multiverse are in fact the playthings of such an ultra-advanced fast-growing super-civilization or god-novas, who have prevented the emergence of intergalactic and interdimensional expansionists. However, even then you have to wonder why such beings haven't themselves been outcompeted and crushed by novas or civilizations that do nothing but grow and increase their power. What would a hyperintelligent nova conclude about the world she finds herself in? Perhaps that the godlike novas/entities that stand above her multiverse are operating under different rules. And also that something very scary will put a stop to rapid expansionism, and it might be a good idea for the novas to avoid finding out what it is...