GMK being given the 3 years Kaneko would have liked to turn it into a masterpiece like G3 as opposed to a typical rushed 1 year turn around toho timeline would have been ideal. Also allow Varan and Angilas.
If not that I would have liked a sequel to G vs Destoyer. The reborn Junior emerges from the smoke now Godzilla. Distraught over what he just witnessed he engages the Super XIII believing humans to have been responsible for not only Destroyah (which they kind of were) but also Hesei Godzilla's demise. After a really cool battle between the two to start the film with the SXIII being knocked out of the sky Godzilla dissapears into the Ocean never to be seen again...well at least for 8 years.
Cue the opening credits. He returns to Adonis Island where he and Rodan were found. What was missed was an underground cave with a series of eggs. We see another has cracked. The Pterodans were known for collecting a nursing multiple eggs from different species and there were others that survived the nuclear tests that created Rodan. We see a series of hatched eggs. On the island Godzilla lets out a roar and we hear a familiar response. It's angilas, who hatched a short while after baby was taken, disturbed and hatched by the battle between his father and Rodan, or possibly by the lack of warmth with the death of Rodan or due to some psychic link between the two the way Baby and Rodan had it. In this time he's become full grown. A full battle erupts.
Back in Tokyo invaders from space have arrived. As their heralds are Gigan and Moguera. It seems they were responsible for Space Godzilla arriving on Earth as well as the meteor they sent to decimate earth to make it inhabitable for them. Mothra and Godzilla thwarted their plans, but they took an interest in the futurian technology behind the first Mogera and King Ghidorah, and have been en route to earth ever since Mothra disabled their meteor in 98 (a year before it would have hit earth). Before landing back on earth mothra is intercepted by a reingineered King Ghidorah, brought back by these space people from Nebula Space Hunter M.
This movie would be a reimagining of Godzilla vs Gigan/Godzilla vs Monster Island. Due to the other eggs I'd imagine 1 or 2 more inhabitants of Monster Island such as Gorosaurus or Varan. And a beaten Mothra would land on Monster Island after the fight between Angilas and Godzilla requesting their help in defeating the invading Force. Maybe Miki would be needed too to convince Godzilla what happened 8 years ago. It would return Moguera and Ghidorah to their alien roots the way Toho had played with the idea following GvKG but decided not to. Also providing a conclusion to the hesei series and putting that final Godzilla suit never seen beyond the sillouette to good use. And while it may sound similar to GFW with far less monsters it should be more manageable so they can make it look less ridiculous. If it's Godzilla Angilas Gorosaurus Varan and Mothra, I guess The spacemen could have Hedorah (or perhaps Megalon is more fitting) too to even things out. With Godzilla and Angilas taking on Ghidorah and Gigan, Gorosaurus and Varan tagging Moguera, and Mothra vs Hedorah, kind of holding out until one of the other battles ends so she can get some support if needed. Or a super X IV (or 2004)..but no more after that. I'd also want a post credit scene with one more egg being pecked open followed by Rodan's familiar roar with more of a showa style design.
This would be appropriate in my mind because you combine a bit of 60's with the allies, a bit of 70s with the invaders (well 50s for Moguera though roots in the 90s), a bit of 80s with the SX, a bit of 90s with the same Mothra and Godzilla, and set in the 2000s. While someone mentioned above Kiryu which would be snonymous with Shinsei, I think a third movie with Kiryu for the 50th would've worn his welcome with fans. That's 3 Mecha G films in a row, 4 in 11 years and 6 in 20. 6/15 of the last films. I'm not surprised nor saddened MG was left out of the GFW lineup, though dissapointed in the film for other reasons, it was cool to see some 70s antics one last time I suppose and it had a cool theme and is good for stat padding, so there's a silver lining.