OK, we're stuck with Tom Cruise then.
Luckily, the story almost writes itself:
Maverick (now top instructor at Top Gun) shows some young hotshots how it's done in awesome aerial sequences. Later, gets on motorbike to visit wife's grave (Kelly McGillis inexplicably unavailable for the sequel)
Doris, a brilliant pilot and daughter of the president of Freedomistan visits Top Gun in some exchange program. Mav and Doris fall in love despite all the odds. News comes through that evil Iran has invaded neighbouring Freedomistan.
While the US cannot officially support Freedomistan for some reason, the CIA allows Mav the use of a C-17 to try to evacuate Doris's family. Peter (Goose's son, that Mav has adopted since Goose's widow was killed in freak auto accident and now happens to be an excellent aircraft mechanic) insists on coming along. They get hit by an Iranian SAM, and Mav brilliantly manages to crash land although all are rendered unconscious.
They wake up in a Zoroastrian monastary in the Iranian mountains. Suddenly, Mav hears 'You!'. It's Iceman who's become a monk (TODO: Fill in some backstory here)
Mav, Doris, Iceman and Peter leave for the border but get captured and taken to an Iranian airbase.
After some brutal interrogation, Mav escapes, frees the others and steals some guns, but they get cornered in a hanger. Under some tarps, they find a bunch of F-14s delivered in the 1970s that the Iranians have allowed to fall into disrepair. Peter gets to work, and manages to get two of them servicable while the others keep the Iranians at bay with special Hollywood unlimited ammunition.
With 'Danger Zone' playing in the background, the hanger doors open and Mav and Iceman (Note for props dept: We may need a bigger cockpit for Val Kilmer this time) head for the runway. Doris and Peter in the RIO seats. They come under intense machine-gun fire, but luckily are not hit.
With their AIM-54 missiles and cannon fire, they manage to shoot down the entire Iranian airforce who appear to be equipped with planes that look a bit like F-5s.
The Iranians 'bug out' from Freedomistan. The End.