Spoilers about the game's story follows.

If you're okay with spoilers, read on.

Here's my theory:

Project Zero Dawn was proposed because Dr. Elisabet Sobeck was NOT an expert on military technology

The game has a hologram recording of generals suggesting they could send unmanned bombers to attack the rogue machines, and Elisabet responded that they could not send anything automated because they would end up getting hacked.

Disregarding the issue that the nanomachines responsible for the Plague can take over electronics of a different architecture and programming language, Elisabet seems to have little knowledge of non-electronic weapon systems that could still make a huge impact against the machines, like nuclear artillery platforms.

Let’s take the in-game strategy of giving recruits railguns, who will end up being just cannon fodder anyway. This is horribly inefficient if you compare the effect of a railgun to a weapon like the M-29 Davy Crockett, a man-portable nuclear launcher. In real life, this weapon was never used because it was a suicidal weapon, but in the context of a robot war apocalypse, this kind of weapon would be critical.

Another alternative would be to send birds, dogs or various other animals to deliver the nuclear payload. No human lives would be lost, though training the animals to hit the right targets would be hard.

Dr. Sobeck, however, did not know about weapons like this (which makes sense because she was never involved in weapons development, and her robotics was focused on peaceful use).

The terrible side-effect of this is that Sobeck couldn’t develop a strategy to exterminate the machines, and instead opted for a risky solution. The generals in the room didn’t mention any of this, because they made the false assumption that Dr. Sobeck already considered the use of portable nukes.

While Elisabet’s plan did work out in the end, it seems apparent to me that Project Zero Dawn was only proposed because Elisabet wasn’t an expert on weapons.

This makes very little sense. This theory hinges on the idea that she was the only person coming up with solutions, which is absurd. The entire world was trying to find a way to win the war, no one could. Her solution was the only option left after the collective force of the entire planet, with all their weapons and weapons experts, failed to find a way defeat the Faro Plague. There are audio logs that mention mass scale nuclear attacks which only managed to hasten the environmental degradation and did little to slow down the robots.

Nuclear scale attacks did very little to stop the waves of machines. They are essentially immune to radiation (besides the few that might get fried in the EMP burst that accompanied the nuclear detonations) so they are free to consume tainted biomass that would otherwise be harmful or useless to humanity. They consume all biomass, charred, dead husks of people and plants included. They reproduce faster than they can be destroyed, which was entirely the problem. Destroying them wasn't an issue, as records show at least one unit in Operation Enduring Victory was able to reliable take down Titan-class (Metal Devils) units, but it still didn't matter. Against an enemy that feels no pain, no hunger, can reproduce indefinitely, and can feed on the land and the dead, humans have very little they can do. Judging by the audio-logs, it was a war of morale and attrition. You can't keep fighting an unstoppable enemy forever.

This also happened in a matter of months. By the time Ted Faro announced that the company would focus on man-driven weapons, it was already too late. Things might have been winnable for the human race if Faro came out at the start of the Hartz-Timor swarm going rogue and sought help from the military and localized to a small area. But he had to wait until robots eating dolphins showed up on the holo-YouTube and more before just reaching out to Elisabet to try and make it go away quietly. By the time Elisabet came up with Zero Dawn, it had to be enacted right away or everything would be lost. The sliver of time they completed everything by meant that no delays or alternative strategies could happen. It had to be "Start Zero Dawn recruitment and building immediately and start Operation Enduring Victory immediately!" We even see just how close things got to being ruined by the sight of the Metal Devil's claw piercing almost into the Cradle complex.

I think Elisabet knew exactly what those weapons could do and knew it would be worthless to try and fight.

Ah, it seems I must have missed those audio logs. Hmm. I still can't help but feel like they could have tried other ways. There were mentions of colony ships that unfortunately didn't finish; could the Fallout vault solution work? The hidden underground facilities seemed to have escaped destruction by the Plague

@mayu_zane: There's a log which says that something happened to the colony ships they built and Elisabet specifically says that Zero Dawn was now the last hope.

The vault solution is essentially how they housed the AIs and also the oft mentioned 'Elysium' that all the scientists would retire to. They had to sterilise themselves however as there wouldn't have been enough food to live long enough to reach the other side. You could make an argument here for why they didn't spend time storing food or finding ways to create it or something :P

I think that solution misses part of the point of the story. The reason Faro killed the Alphas and destroyed the education arm of the plan was because the evolution of weapons to destroy weapons is what lead them to this end. If you think of it from that perspective Elizabet's plan is the best way to move forward. We see it in the real world. Making weapons to scare people from using weapons doesn't actually work.

The reason why Faro killed the alphas and erased all copies of APOLLO is because he didn't want to go down in history as the man who killed the world. All this talk about the next generation of humans not repeating their mistakes were lies that he told the alphas, and perhaps over time he even convinced himself they were his actual motivations, but to me his motivations were clearly egocentric. His narcissism drove most of his decisions in life and after that led to the destruction of all life he'd much rather the world forget that he was the cause of this than to remember the past and have the name of Ted Faro be on the same level as Satan.

On a slightly different subject, when it comes to the DLC for Horizon: Zero Dawn, what do you think will be its subject?

Personally I feel like a good portion of the DLC will surround the Subject of APOLLO. Piecing together various journal entries and audio logs in the game, I have figured out that there still is an early copy of the APOLLO software that still might be intact. It was sent onboard the Failed Odyssey space ship that was built to try to colonize other worlds. The journals say that the Odyssey never left orbit and is most likely still up in orbit. The question is did Ted Faro know about this copy of APOLLO, and if he did was he insecure enough to try to erase the Software on a failed space ghostship that would never go anywhere?

@darklingscribe: The journals don't just say that odyssey never left orbit, but that it was destroyed in some sort of "antimatter explosion" or something. I doubt any part of the craft survived, but they do leave the particulars of that as pretty vague, and even if it had after 1000 years it's feasible its orbit deteriorated enough to crash it. Maybe recovering something from a crashed ship will be part of the DLC/sequel? Also possible that Faro didn't erase all copies of Apollo, the game makes him out as a bit of an idiot. Maybe HADES has some of the Apollo info, or how else would he have taught Sylens so much?