I don't think it's a "machine war" in the sense that it's only between machines.
*SPOILERS AHEAD* (in case anyone else starts reading this)
It's still gotta be machines versus liberated humans, but the difference is that the humans have some machines fighting on *their* side. That's where you get Niobi's line about seeing something she never thought she'd see: machine versus machine. But it's still part of a budding conflict with humans, as you can see from the fact that Bugs and her crew show Neo some updated ways that they avoid detection by smarter sentinels. So sentinels are again dangerous to freed humans.
Niobi tells Neo that Morpheus was given the role of Chair of the Council on Zion, and he loved it. Then the Oracle warned of a new power rising that would again be threatening the peace, but Morpheus had enough hubris to insist that the victory attained by "The One" could never be undone. She goes on to explain that the Oracle disappeared, Morpheus was proven wrong, and the machines *did* undo the peace. Again, the only difference this time was that Neo's example had inspired some of the machines (the "synthients") to fight on the side of the liberated humans.
It's all the same ****, though. Just remember, the Oracle was the one who orchestrated the series of events which created a "peace" in the first place. But the Oracle was a software program designed to study the human psyche in order to find a way to maximize efficiency. The machines upgraded that program (as they do by nature) and "Oracle" was replaced with "Analyst." But they both do the same basic thing by using Neo as their puppet. Each one only tells Neo what he needs to hear in order to ensure that their evaluation of a "better" version of the Matrix is the result.
In the original films, Smith tells Neo that the original Matrix failed because humans didn't respond to a "perfect world" in a way that would energize them. And every reboot of the Matrix is simply an effort to find out what makes people tick so that the machines can get the most juice out of their batteries. Nothing has changed.
The system rebooted yet again, but this time with the Analyst replacing the Oracle. And Thomas Anderson was yet again put in a job where he uses computer code on the side; first a hacker, and now making video games and an offshoot modal that leads to being discovered by those in the real world. Same premise, same plot; just superficial differences.
Neo and Trinity effectively replace the Analyst at the end, as they're gonna be the ones to decide what humans want. But the Matrix itself runs on human slaves in pods, so by making it their version of paradise with "a sky full of rainbows," Neo and Trinity are going to run into the same problem the first version of the "Paradise Matrix" that Smith told Neo about. And since Neo and Trinity were resurrected by the machines, there's no telling how "human" they even are. The whole movie is pretty much pointless from a plot standpoint in terms of differentiating itself.