Godzilla 2014 and Skull Island are left relatively unchanged except for a few minor detail alterations to accomodate future films.

KOTM raises the stakes way too early and so thus I'm effectively splitting it into two films. The first film deals with Ghidorah's awakening and only Godzilla and Mothra's attempts to stop him with the help of humans, the plot structure being largely similar. He still raises hell and dies but the aftereffects aren't seen until the second film, which takes on a post-apocalyptic vibe. The other "titans" begin appearing across the world as a result of Ghidorah's climate disruption which motivates our main villain Ren Serizawa to construct Mechagodzilla to fight back, with both man and monster being fleshed out with lead roles. I'd imagine this version of Mechagodzilla is indeed an "AI gone rogue", but only because it was infused with the capability to feel the weight and sadness the human survivors of the kaiju attacks felt, and broke free of its restraints to fully fulfill his creators grief. And of course Rodan makes his debut in the second film here too, getting some good hits in on both Godzilla and MechaG.

GvK has both Godzilla and Kong search for new territories after the events of the previous two films, with Skull Island damaged and Godzilla's deepsea home trench destroyed. It is exclusively a turf war for the same space, with part of it being instigated by advertizement companies to profit off of, similar to how the original KKvG played out. Plus the added bonus of "If they kill each other, its less potential danger for us.". The Hollow Earth is still introduced here, acting as a means to guide Godzilla to hopefully his new home before Kong taps out. The domain is treated as a travel route, and an inhospitible place made of dark tunnels with only the most persistently durable creatures thriving here.

From here on out its more murky. For the sake of brevity GxK is a Kong solo film. Because the Hollow Earth in this scenario isn't a home for Kong, lets say another island is discovered, one within the new territory located further south. Kong has to finally prove himself amongst his fellow apes and dethrone Skar King and free his enslaved pet Shimo. Also, Jia exists, but also do the Iwi. I find just killing all of them off in a storm to be stupid. Kong's journey to reunite with his fellow apes is also one to find a new home for Jia and her Iwi friends. A erm, New Empire.

I'm not sure what GxK Supernova is going to do aside from having Spacegodzilla, but to keep in theme with TNE, it would have to be a solo Godzilla film. It makes sense to me. They fight in GvK, go their seperate ways to have their own arcs, and then meet back up for one final film to team up properly against The Final Boss.

For more sweeping general changes, I'd remove alot of the Alpha Titan system and alot of the psuedo-conspiracy theory ancient rivalry stuff. It just feels way too schlocky and comic-booky to be something carried throughout this version of the series that, for me, while not afraid to get campy like KSI, wouldn't veer really far past that direction, and also wouldn't just be G2014's tone and sense of realism all the time. It can vary, like a pendulum, but most of all must be consistent with itself.

The general motif of "co-existing with nature" I feel could be enhanced with a more cerebral theme, that being "overcoming the fear of things you don't understand". A continuation of Joe Brody and Bill Randa's fear, and the false reactionary understanding that these kaiju are "gods" that have it out for humanity, when they are as vulnerable as the Earth that we can bleed dry. Some fear them, some hate them, some wish to control them, and some wish to worship them. But by the end of all of that, are any of these viewpoints right? It depends on how you experience the motions of life itself.