First, let's start with the movie's surprise ending. Lena is the sole survivor of the team that went into the shimmer, and she's getting grilled about what happened. We know there was all sorts of mixing and scrambling of DNA/body characteristics inside the shimmer, so she's not exactly the same Lena that went in. For example, she now has Anya's tattoo on forearm. But her phosphorus-grenade trick in the lighthouse resulted in the whole shimmer/alien presence being obliterated. No more scrambling. Even the alien-Kane is now stable. So, maybe, in the end, everything is going to be OK. Alien-Kane could just be a human clone, with a rough imprinting of the real Kane's personality. Life can go back to something approaching normal. But then she goes to see him.
What? She's hugging him? She knows he's an alien! It's not her real husband! But then the worst happens: we see a strange glow in alien-Kane's eyes---he's not fully human now after all---and then the same glow appears in Lena's eyes. No! Not her too!
We saw that glow in Lena's eyes during the encounter with the glowing ball of alien presence in the lighthouse, when it sucked out some blood from the corner of her eye, and proceeded to use her cells to grow the prototype of an alien-Lena. Then it could have just been a reflection of what she was looking at. But now we see more was happening: she was getting alienized!
And now, at the end of the film, instead of "happily ever after," we have alien Adam and Eve. Look out humans! The real annihilation is about to start!
To me, this makes some of the strange pieces fall into place. Why the alien copies of Kane and Lena? Why did the burning alien copy of Lena purposely go around the lighthouse setting fire to everything connected with the alien presence? What was the point of all the scrambling of life forms?
I think of the meteor at the beginning as a spore from some vast alien entity, spreading across the universe, taking over everything in its path. Now it is infecting Earth. It grows and develops along a pre-programmed, almost mechanical path, doing what it does, like a basic biological entity, a seed in the ground germinating. Like Ventress says, it doesn't really want anything. It's just going to keep growing the shimmer and scrambling everything until the end. That's what it's programmed to do. Yes, it has a mind, of sorts, that connects with the vast whole, but it operates in a very different way, like some sentient super-fungus.
So, how does it take over planets? The spore lands, and creates the growing shimmer, inside of which everything is getting DNA chunks/bodily forms randomly swapped. The shimmer grows and grows, and will take over the whole planet unchecked. But, really, it's waiting, like those trees that make seeds that can only sprout after a forest fire. In this case it's waiting for the planet's top species to come kill it.
Anything that comes in has to run the gauntlet of strange beasts, disorientation, rapid mutations, etc., to be able to get to the lighthouse, which is the flowering body of this organism. Anyone that gets to the lighthouse has an edge on the others. They are a good example of the top species, and so they get copied, with an added dollop of alien mind-connectedness. But they have a very short shelf life: alien-Kane starts to disintegrate quickly after leaving the shimmer. This simple copying will keep going on to anyone who enters the lighthouse. (Presumably Ventress was rejected as too close to death.) What it's waiting for is for someone who has evolved to be fit enough, wily and resourceful enough to beat it. That's the one the alien really wants for its next life stage.
So, when Lena outsmarts her copy with the phosphorus grenade, the spore has accomplished its mission. She is the One! That's why the burning copy goes around destroying every trace of the spore apparatus. It's like getting rid of the afterbirth. Now the alien entity has a super-evolved, top-species-on-the-planet, alien-mind-connected organism to work through. Not only that, but any other of the alien copies of the top species that are still alive will also be available. And so, in our case, we have alien-Kane and Lena, ready to start breeding, and taking over Earth with alien-connected humanoids.
Presumably, spores like this could work on other planets that have a top species smart enough to kill them. Without being intelligent in the usual sense, it creates/selects top specimens simply through its design, and then disappears, leaving alien-connected versions of these top specimens, who will then go on to overwhelm the planet. Clever idea!