In some of them he already has. There are variations of AoA out there (AoA What Ifs) which are alternate universes/timelines (like the universe Deadpool jumped to in Cable/Deadpool), as well as the Cable/Stryfe native he had conquered. I think the confusion comes from the fact he rules alternate futures when most of the storytelling is done from the mainstream current.
I just find the whole "Apocalypse hasn't accomplished anything/Apocalypse always loses" argument hollow and frustrating because it seems to overlook the caveat that his conquest of Earth has always been depicted as being in the future, and that is due to certain benchmarks needing to be met before he enacts his takeover of a world where mutants are a majority of the world's population. Patient stewardship of evolution is his central character theme.