In the '62 KKvsG, Godzilla was a straight bad guy so having Kong fight him kinda made sense. In Legendary's timeline, both Godzilla and Kong are "protectors" of their respective worlds so it seems more far fetched (in my opinion anyway) for them to fight to the death. A prolonged primal brawl, perhaps set up by humans, followed by them setting aside their differences to team up against a common enemy works better for the universe they've set up (again, IMO).
Hell, they could re-title it GODZILLA AND KONG: DESTROY ALL MONSTERS. Problem solved.





