I can see with Anno and Higuchi in this, a strong scifi element and strong human characters.
I could easily see a story about a 26 year old woman and 7 year old son who's grandparents (great grand parents) were from Oto Island and witnessed Godzilla's first attack. This woman is trying her best at being an amateur journalist and is primarily thinking mostly of herself while her son is along for the ride. Her husband left her for being overly selfish and she has moved out onto a smaller island so her aunt can help raise her son as she's working on assembling information on a possible case for a big story about illegal nuclear fuel dumping. Possibly one of China's new nuclear subs washes upon a beach in wreckage. Insert international incident here and the UN gets involved, while now with her attention on this, the main character also finds out via BBs boards that two Russians subs have gone missing in the last year years and a few wrecked boats have been discovered exposed to massive radiation. The thing closely resembling it? The original G54 incident. She comes into contact with a poster on one board and gets correspondence about the subject and decides to meet said hacker who goes by the screen name "M-11". She meets with said hacker and gets information that Godzilla is alive and the governments are well aware of this, but keep mum to avoid public terror. On the way back home, she is pursued by agents of the govt and is rescued by several people who turn out to belong to a cult that worship Godzilla. They kidnap her son and transport them to Otot island where they are based and on one night they come onto the beach to witness the rise of Godzilla-and end up being attacked by a titanic, mutant boar (25 meters long) before Godzilla rears his head (although obscured mostly by fog and rain) and slays said boar easily. The rest of the film involves Godzilla vs the military and Japan's recent new weapons the Iron Beetle amphibious tank and the Super- X Delta prototype vehicle. The main character learns that she has to stop being reckless and actually take responsibility for her son and her actions and it turns out a relative of hers is the scientist that helps build a new Oxygen Destroyer that is deployed on land. It fails in killing Godzilla, but kills a large population of civilians. Godzilla is triumphant and plods away feeding off the Iron Beetle and Super X-Delta's nuclear batteries.
Or maybe another plot could be like:
The plot focuses on a think tank of brilliant late teenagers that is sponsored by the US and Japanese governments. Strange occurrences drive one student to start to put together things that include: a severe volcanic event along the Japanese coastline, irradiated sea water, several ships disappearing, two subs going missing, and sea animals washing up on the beach in several large groups and being irradiated. He believes Godzilla from 1954 is back. It is confirmed though when he hacks into the "BLACK files" of the Japanese government. He finds evidence of a larger, more powerful Godzilla destroying a Japanese destroyer from ten days earlier. Amongst these files he finds photos of a Russian kaiju called Anguiras, and a kaiju sighted in Sakhalin called Varan from 1986. The strangest thing is evidence of alien ships over various nuclear plants throughout decades. All this stuff is inconsequential, Godzilla is the threat. Days later he is approached by the Japanese government after the Japanese military filmed a confrontation between Godzilla and their fleet, Godzilla turns out it was hunting/battling a kaiju called Maguma. The government wants him and his thinktank to use recreate the Oxygen Destroyer. The group tries and its outfitted on an experimental aircraft. They get their chance when Godzilla makes landfalls, and yes he leaves few trilobites behind and the O2 Destroyer is deployed-but doesn't harm Godzilla on land, but it kills a few hundred people and critically injures a few more hundred. Then a bizzare alien ship arrives and uses a sonic weapon to force Godzilla back to sea. The ship belongs to a race calling themselves the Kilaaks and they reveal things about Godzilla. This race was at their height when the dinosaurs went extinct, but they reveal something new about the two Godzillas (the one now and the 54 one). The radiation of the Earth was higher during the age of dinosaurs, but the asteroid that wiped the dinosaurs out caused some dinosaurs to burrow or go undersea, but because of the asteroid striking and breaching the crust it spewed radioactive debris into the atmosphere that causes some creatures to mutate, but eventually these creatures (as radiation levels leveled off) went into suspended animation. Nuclear testing in the modern day and waste dumping awakened and further mutated them. The Kilaaks are quite interested in Godzilla because they believe his mutation is something to be studied, but they wish also to help mankind against him. Throughout the film the thinktank and the main character gather new info about Godzilla: that his regeneration is exceeding powerful/fast, his bones are possibly the most dense/powerful substance known to man, and that his skin tissue is exceedingly thick and resilient. Then in the last 25 minutes, it is revealed that the Kilaaks are the last of their kind, they have been a relic species that stayed on Earth as the rest of their kind became extinct.
These mineral based creatures have became one in the same with their AI and now are a gestalt intelligence. They want to destroy Godzilla so they can war against man and destroy 95% of the human species and take the remnants and convert them into a Kilaak-like race. They believe mankind's religions, individuality, artistic-creativity are road blocks top become a perfect species and they wish to destroy man's culture. The main character now, must instead of acting selfish and using his knowledge for his own gain must unite his peers to fight this threat. Godzilla arrives when the thinktank hack a power plant and make it vent radiation to attract the creature and Godzilla arrives and ends up facing a Kilaak kaiju (new one) and winnings before turning his attention to the Kilaaks. The Kilaaks are destroyed almost entirely before the last few realize they are fighting futility and self destruct. Godzilla destroys the plant and returns to the sea as mankind realizes that its great enemy has helped save the from an existential threat.
How about that stuff?