For example:
Processes and tools can often be one of the best ways to improve interactions among individuals. See Scrum, which is hardly a panacea but sometimes it works wonders.
For a large project, comprehensive documentation is essential to producing working software. Ideally the documentation should be so comprehensive that it pervades the very fabric of your application in the form of good factoring, command-query separation, etc.
Contract negotiation can be an important first step in customer collaboration. Everyone needs to know where everyone else's needs, boundaries and comfort zones are.
Without a clear plan, how can you be sure of the best way to respond to change? See: Duke Nukem Forever, WinFS, RIM.
"I'm willing to give up some valuable-thing-Y in exchange for more X" is a textbook example of a tradeoff.
"We value X over Y" is not a trade off, it's a dogmatic claim.
"We should do X in these conditions and Y otherwise" is a trade off.
For each of the items you list above, I can come up with a few scenarios where doing the opposite of what the Agile Manifesto says would be the better approach (and that's probably one of the main reasons why hardly anyone takes that Manifesto seriously these days).