Ill try to do miy prediction:
Ending 1: The salvator
Neo and company fight till the ends against the machines.......morpheus and a lot of civilian dies when the machines attack Zion.........
in a desesperate battle,,,neo finds the "mother core" of all the machines....or maybe he travel to the machines´s city (showed in the animatrix series), and destru them all with his rare powers.
At the end just a few humans survive from the battle,,, and they will fight to bring life again to the devastated world. Trinity gave birth to a neo´s son that will be the king of human kind.
Ending 2:Holy punishment
In the final battle, the humans were bravely fighting with the machines,,and in the battle a lot of people died. IN the middle of the first battle, GOD himself desesperate after seing all the things that the human were capable to do to themselves,,,decide to destroy the earth and end his most debatable cration, the humans. (dont know how this will be).
Ending 3: Re-reloaded
The machines destroy zion, neo uses his powers to beat almost all the machines, and rescue some of the people in zion to make a new world.
But no one was aware that the amchines, a little group, were still alive,,, and they prepared themselves to doa nother and new matrix.
And the movie have that end like it will be a 4 movie .