I tend to choose the versions having version exclusives (not only legendaries) I like more than others. That's why I choose White/White 2 over Black/Black 2 because I liked it's version exclusives more and they overweight the Black's version exclusive Pokémon.
I had the feeling since the beginning I would get maybe the Sun version and given the version exclusive like the rugby lemur or Rockruff's Sun evolution appealed to me. Like Gen 4 I wasn't sure which legendary I would like, but judging from the version exclusives helped me. I like Lunala, but somehow I feel drawn to Solgaleo more. The time difference between Sun and Moon sounds nice, but I prefer to play with the timezone I'm familiar - so it's Sun.
Version exclusives can be traded over, but the differences (from my view) between both versions could be seen in the mainstory like which Totem Pokémon or Ultra Beast could appear.