The ending?

my opinion is "sequel".

The ending hints at absolutely nothing. Remember that this movie is directed in such a way to resemble a graphic novel. So anything that you see, which should have been painfully obvious from the lack of story telling elements, is irrelevant. Only dialog matters.

So watching the machine flying towards mars is just a fancy attempt at a "cool" looking image. As with every other scene, it was over elaborate and encorporating as many references to previous dialog as possible. This movie TRIED to be a comic book and failed miserably. Remember when Samuel saw fire coming from the elevator towards him. Any other movie would indicate that Samuel was injured by that fire or that that specific death affected Samuel deeply. Fact of the matter is that neither concepts were true because seeing something through the reflection of the eye was never meant to have meaning. It was only meant to look "cool."

So that being said, there is not reason to accept any images from this movie at face value. The dialog said that humanity was saved, we have to assume that that is what happened. The ending scene be damned!

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Babies:
Fun to make
Even more fun to eat

I have to agree with what srcliffrd said in another thread:

"I think it was probably the CPU or maybe organism that ran the mutant production plant. It had a "return to sender" or maybe "go on to the next inhabited planet" program built into it that the heros activate at the end. As to why it had that function built in, my guess is that the last mutant created was meant to trigger it because the mutant maker would no longer be needed."
http://www.imdb.com/title/tt0490181/board/thread/144165489?d=144260284&p=1#144260284

So the machine only "thinks" about making mutants not if the humans deserve it or not..
And if you by the ancient mean the human tribes, I don't think they knew how to program anything about it, which was why they sealed it in and just took "the bomb" with them to the surface...