I could see Rodan and/or Anguirus being used as other dinosaurs mutated by nuclear or biological weapons tests alongside Godzilla. It could tap into the radioactive dinosaur cliche, perhaps having the story set in Japan.
Ghidorah would be nice, but I can't think of a way to use him that wouldn't change his or Godzilla's origin. Godzilla is a mutant dinosaur, Ghidorah is a planet destroying space dragon. IF a story can be made that is true to both, than sure.
I myself have been working up a story idea for the film. The villain is Battra. The basic plot of the film has the world in a massive arms race (like Godzilla vs. Biollante) 60 years after the 1954 Godzilla attack. Someone gets the bright idea of cloning Godzilla to counter nuclear weapons. Cloned from preserved skin cells found in the ruins of Tokyo, Godzilla forms a bond with a female Japanese scientist (played by Rinko Kikuchi) Godzilla is able to absorb and purify radiation, potentially making nuclear weapons useless (much like the ANEB).
However, the lab containing Godzilla is attacked by a terrorist group called Black Moth. Godzilla escapes and several G-Cells are stolen. The governments of the world meet (Japanese Prime Minister is played by Akira Takarada) and decide to destroy Godzilla. Meanwhile, Black Moth has created Battra from the stolen Godzilla DNA. Godzilla fights the military (using battleships and maser cannons). Godzilla is calmed down by Japanese scientist, but leaves as if sensing something. Godzilla heads to an island off the shore of the northwest United States where he fights Battra's larval form. Both monsters are injured, Godzilla going dormant and Battra fleeing underground.
Both monsters recover, Battra metamorphosis into its Imago form and the monsters have a rematch in Seattle.
In terms of Battra itself, it is now a living doomsday weapon created from Godzilla's DNA. One of the main changes is its size. Godzilla is about 120 feet tall and is 250 feet long when layed down from snout to tail. Battra's larval form is almost as tall as Godzilla when it raises up (not counting the horn) and is about 300 feet long. The Imago form is also larger than Godzilla, the body being almost as big as him and having a 300 foot wingspan.
As for powers, Battra's larval form attacks mainly with its horn and tail, as well as some constricting abilities. It can also fire bio-electric bolts from its horn and burrow underground. The imago form fires stingers from its abdomen (like GMK Mothra) and instead of laser vision, it sprays acid from its eyes, like how a horned lizard sprays blood from its eyes.
Battra's larval from is more of a brutal, close quarters fighter, the Imago form more of a ranged combatant due to more weapons and flight.
I also changed Battra's roar. Instead of the Rodan like cackle, it has more of a raspy scream, kind of like this:http://www.youtube.com/watch?v=2AWYIAdI ... plpp_video