One thing I've noticed as I add more faction mods: the core sector expands. You have to go farther start exploring. You have to go farther to find pirate and pather bases, and you often end up with a bizarre tangle where one faction's systems are under pirate threat from a base that's completely on the far side of the core.
In vanilla, not only is the core sector relatively small, it also has three (that I can think of offhand) partially-handcrafted uninhabited systems: Duzahk, Penelope's Star, and Nia Tahl. It would be nice if some faction mods would follow suit, mixing a spare empty system in with their faction's systems.