The latter two films are a mess, for sure, but to give my thoughts:
So did he really accomplish anything that makes any difference in the long term?
The conceit of the latter two films is that the Matrix is cyclical. (A microcosm of the idea that all time is cyclical). Neo is not a bug in the Matrix, he is a feature. He's like an internal PenTester. He exists to show the machines how The Matrix can be broken. Then they rebuild the Matrix from the ground up, accounting for the flaws Neo revealed to them. Then they create a new Neo to test for flaws in the current version of the Matrix. Thus the Matrix is made better each time.
Neo's accomplishment in the films is to break that cycle, and make a truce with the machines. The war, and the subjugation of humanity that followed it, are officially "over." But there's a lot of room for shit to get fucked up. War doesn't end overnight. But Neo created a chance at a new beginning for homo-machine relations.
Who was the spiky head Neo met in the machine city?
The leader of the machines. The biggest, smartest AI, which chose to present itself in the style of The Great and Powerful Oz.
And what really happened in the end, and why didn't Smith foresee it?
I'm having a bit of a hard time remembering exactly how this went down, it's been a couple years since I last watched the films.
So Neo lets Smith assimilate him, and this causes Smith to be destroyed, right? Given how much Christian allegory there is in the third film, I'd say this represents the 3 days Jesus spent in Hell. In Christian mythology, Jesus dies on the cross, "Descended into hell," and rose from the dead 3 days later. And in doing so, he threw open the gates of heaven, and led all of the souls that had been trapped in Limbo to their eternal reward. In the same way, Neo is consumed by Smith, and in doing so, frees all of the people who had been trapped by Smith.
In fact (and I'm completely guessing here. I don't have a copy of the movie I can check ATM), I'd bet you dollars to donuts that there's some kind of 3 beat between Neo being assimilated and Smith being destroyed. Something to stand in for the 3 days Jesus was dead. Like maybe Smith laughs 3 times or something.
They kill a bunch of humans and somehow that's okay because of the Matrix, but they are still innocent and they still die, and real people still grieve them!
There are a hundred thousand different ways you could interpret this.
- Perhaps it demonstrates that humans are still the brutes who scorched the sky when we fought a war with the machines. We're willing to suffer any loss if it means winning. It begs the question of whether we even deserve the freedom we're fighting for.
- Perhaps it asks us to empathize with a terrorist mindset. Yes, killing innocent people is bad. But when we put you into the shoes of these characters, can you see how killing innocent people might seem like a reasonable choice?
- There's a quote from the TV show M*A*S*H that gets thrown around the Internet a lot:
"War isn't hell. War is war and Hell is Hell, and of the two, war is a lot worse."
"Why do you say that?"
"Who goes to hell?"
"Sinners, I believe."
"Exactly. There are no innocent bystanders in Hell. But war is chock full of them. Little kids, cripples, old ladies. In fact, except for a few of the brass, almost everybody involved is an innocent bystander."
In the Matrix, when you shoot at an agent, you're shooting at the enemy. But if you succeed, then the enemy doesn't die. An innocent person dies. Someone with hopes, dreams, a family, people who love them. Because that's what happens in all wars.