Perhaps intergalactic distance is simply the result of physics, or perhaps it reflects preternatural logic. Assuming (as scientists currently do) that there cannot be faster-than-light travel, galaxies separated by distances in the millions of light-years will never be able to have any form of intercourse with each other: no weapon one could make could strike the other, and no invasion could ever be launched.
Considering the track record of mutual hostility and misunderstanding in our world alone, where there is but a single species, imagine the havoc if intelligent races from across the galaxies could war on one another. Because of the sheer expanse of intergalactic space, conflict between regions of the cosmos may simply always be impossible, leaving each galaxy to the fate that its own inhabitants determine - not necessarily such a bad arrangement if you're building a universe.