Watching Godzilla vs. Kong again today, my opinion still stands, in spite of some problems I still really enjoy it for what it is. A movie more for the kaiju fandom in general but otherwise fun timewaster for the general audience if they're only going in for the monster action.
My biggest gripe with the movie is how its pretty much two movies mashed together which I do understand as Legendary's contract was due and weren't certain if this film would be a success. But regardless if I had it my way I would have the Godzilla subplot be Godzilla 3 then the hollow earth being Kong 2.
My idea for Godzilla vs. Kong would have pretty much been the first 45-50 minutes of the film minus Godzilla's side of the story that way it could have focused more on the vs. title of the film. It being about trying to relocate Kong to the hollow earth as his new home all while having to try and avoid Godzilla hellbent on trying to hunt down and kill Kong due to sensing their species ancient rivalry, as well as the threat Kong poses to his alpha status being also an alpha himself so Kong has to protect himself from Godzilla and human characters also trying to protect him.
First fight would be as seen in the film in the Tasman Sea, then the second fight being in either Sydney, Australia or Wellington, New Zealand (I'd like this one as it'd be a new location for a kaiju film) as a pitstop to rethink their strategy and resupply (Citizens gathering around admiring Kong, during their fight you could even have Kong trying to bring Godzilla out of the city to avoid civilians deaths since as shown Kong cares for the lives of innocents as he did with the Iwi's, Jia, and Weaver) then the final battle in Antarctica. Like in the film Godzilla would still win but would then somehow find out the humans with Kong are trying to bring him to the hollow earth as his new home and so spares his life as long as he stays down there as the surface is his to rule.
After rethinking this is how I would have done it.
Godzilla (2014)
Kong: Skull Island
Godzilla: King of the Monsters
Godzilla vs. Kong
Godzilla 3 (Godzilla subplot in Godzilla vs. Kong)
Kong 2: Hollow Earth (Focuses around the origin of titans, exploration of the hollow earth, Kong's species notably the temple and such)
Never the less, I'm still happy with what we have gotten so far with the MonsterVerse.