The end could have seen Saleem and Shiva engage in a battle in the decrepit building in which the 420 odd midnight's children have been taken to have their powers 'operated' out. And though Shiva has his powers intact and Saleem and others do not, they somehow manage to put their differences aside, gather force and defeat Shiva in an epic battle more of brains than of brawns.
This fits in with what happened after the Emergency when the opposition gathered forces to defeat Indira Gandhi in elections (of course, they lost it to infighting almost as instantly).
The movie, however, wouldn't have ended here. For the end would have revealed the mother of all twists with 'The Widow' from the book i.e. Indira Gandhi, now no longer in power, finding Saleem and the two have a showdown. Here, Mrs Gandhi would have revealed to Saleem that every midnight of history had given birth to its own 'Midnight's Children' with powers to change the destiny of the nation.
She could have told him that it was other midnight's children like him who had worked with her father to not only win India its independence but also to ensure its future and the uninterrupted, though just rule of Nehru after independence.