The Manifesto was a strong document. It has some serious flaws though.
For one, it does not explain the intention or thinking behind each value. As a result, people misinterpret the values. E.g., "Individuals and interactions over processes and tools" - that is a great value, but if a tool is critical for, say, a deployment, and the tool is down, then guess what? The tool then becomes most important.
So it depends.
And the focus on face-to-face communication diminished the value of written communication - but written communication has immense value.
And the Manifesto led people to think that there is a "best way" for everyone. But people differ in how they communicate and work best.
Also, what about data? The Manifesto mentions software, but not data. OMG, talk about missing the elephant in the room.
And it completely misses the critical importance of leadership. Leadership is arguably the _MOST_ important thing in any multi-person effort. But the Manifesto is anti-leadership to a large degree - a real dysfunction. People in a team are not autonomous - otherwise, it would not be a team. And teams are not autonomous - otherwise, they are not in an organization. What matters is that leadership styles are empowering and supportive - good leadership, not no leadership.
While the Manifesto had some good stuff in it, it is very flawed. That is why Agile 2 was created - to take a more thoughtful and careful approach to the problem of how to achieve organizational agility.