Why didn't the machines clear the skies?

Per my own answer over on Scifi:SE, The screenplay for Matrix Revolutions makes it abundantly clear that the clouds unleashed in 'Operation Dark Storm' are comprised of "molecular replicators" which are totally hostile to the machines. When entering (or even approaching) the cloud layer, the sentinels are instantly "drained of life", then struck by bolts of high-powered lightning.

We can assume that any attempt to dismantle this layer would be a monumentally difficult task. Not only would they be unable to even approach the clouds but since the layer is comprised of "replicators", it seems pretty likely that when you try to destroy them, they ... y'know ... replicate:

Scene 737 : EXT. BLACK SKY - NIGHT

Rocketing towards the churning black sky, leaving a white-hot jet trail that cuts up from the black earth at a forty-five degree angle.

Several Sentinels leap from the back of the ship, but many remain as it barrels towards the dark roiling ceiling.

The Logos plunges into the sky with a surreal splash, like a plane crashing into a sea of shaving cream.

The molecular replicators immediately drain the life from the Sentinels and they fall dead tearing through the clouds that cling to them momentarily like shredded pieces of parachute, before letting them fall away.

The Logos is engulfed by a ball of lightning as it is attacked by the sky. It shakes violently, every light blowing out, until the ship dies

One thought: The machines wanted to kill 2 birds with one stone. They wanted to solve the energy-source problem AND the human problem. Because if they fixed the skies, but didn't enslave the humans, then the humans would just go and do something else to muck things up for the machines. Plus, the machines might have "done the math" and found that humans are a much better source of energy anyway. So:

1. If they fixed the skies but didn't deal with the humans, the humans would mess up their energy source again another way.

2. If they just killed humans, and then cleared the skies to restore their solar power source, that would take a lot of work.

3. If they captured humans and used THEM as the power source, and forgot about the skies, that would solve the human problem AND the energy problem while not taking as much work as option 2.

I don't have proof of this but it makes sense to me!

It's likely that the point in time where the story is, the machines are still working on clearing the skies. At the same time they can't spend all their resources on it because of the Zion/Neo problem that they are trying to solve and keep under control.

So it’s clear there’s a permanent EMP field blocking access to the sky for the machines.

It seems clear that the machines would thrive in space and had achieved a near technological singularity (described in the Animatrix). Their technological advancement was the actual cause of the scorching of the sky as human nations could not economically compete with 01 (the machine city-state)

Humanity initially bombarded 01 with nukes then scorched the sky when the robots started owning humanity in the opening of the Machine War.

So why wouldn’t the machines, who were able to make themselves completely solar powered and self sufficient, prioritize even just a poking a hole in the sky so that they could just get into space? and presumably they could have easily designed jet propulsion systems that would allow them to move about in space. They could have settled the whole solar system by the time matrix revolutions ended, and could have just left humanity to go extinct.

These are not actual questions- obviously there wouldn’t be a story with good and evil and heroes and villains in it if this was all true (it’s a fictional story so it’s moot to make claims about what is “really” true or not, you can only make claims about what is true according to canon). This is a plot hole however, as it is never explained how an AI could achieve economic domination over the entire global market and develop defenses that could withstand a sustained nuclear bombardment, not to mention create The Matrix, yet it just could not ever figure out how to fix the sky. Again, it seems plausible that you could at least create an opening in the EMP field around earth, fly out one self replicating robot, and then the machines are pretty much just the Borg from Star Trek…