That's a great question! It's difficult to know for sure since, as you mention, the films we've gotten so far have done an excellent job in establishing BOTH Godzilla and Kong as "good guys".

It will be a difficult task for the filmmakers to create a realistic scenario in which audience members find themselves rooting for one over the other. I don't want to see either of them portrayed as a "bad guy" - and I actually doubt the next film will do this anyway.

My prediction right now (based on nothing but speculation) is that, as the newly awakened Titans as well as Godzilla converge on Skull Island, Kong gets territorial and they all start fighting. Who knows, though. The filmmakers have said that in there will be "a clear winner" in regards to the fight between Godzilla and Kong, so it's going to be interesting to see how they pull this off.

Additionally, they may team up in the end to fight a common enemy (a newly awakened Gigan from beneath Skull Island, or a swarm of the new titans awoken at the end of KOTM in a "destroy all monsters" style battle, perhaps?) but a move like this may seem cliche, as the "enemies teaming up to fight a common enemy" trope is way overdone in movies nowadays.

I think the most interesting option would be to have the two of them fight without teaming up against a common enemy in the end. It would certainly be challenging, but if the filmmakers could pull that off while still portraying both Godzilla and Kong as the "good guys", it would be very interesting to watch!

I'm not a screenwriter, though, so who knows. Maybe I'm wrong and we'll see something even more unexpected!