I strongly suggest letting waves hit multiple locations. Getting 12K ships from one wave set (4 waves for a 2 player game, about 2K ships per wave, but doubled for the vicious raider) on one planet at 250-300 AIP, can be worse than Exo-galactic strikes.
Assuming you coordinate, split targets means you can both send your fighters to deal with the bomber wave on target B and your bombers to deal with the missile frigates on target A. Of course, since you have double the number of waves.. you may need to do this to survive.
At 4 players during the mid/end game, you really want 8-12 "likely" targets with a reasonable distribution of forts, mines, & turrets etc, and you take everything adjacent to, and heavily defend your factory 4's, your homeworlds etc.