Should I replace my trunk-and-branch setup with a PEX manifold?
If you increase the diameter of the branch you also increase the time it takes for you to get hot water.  In my climate I also like to get ground temperature water so having large branch lines increases the amount of water I have to dump before I get rid of the water in the pipe from the supply entrance to my faucet.  This also wastes heat as the branch lines will have hot/cold water and heat or cool the wall spaces - eventually heating or cooling your house.  

I like the manifold arrangement but one quick thing to try would be to just plumb the washing machine into the end of the branch line.  I this this would allow the other fixtures to have pressure preference over it.   

The other thing I'd do is eliminate the crazy 90s if you are redoing a section.  The plumbing might look neat but you loose significant flow when you make sharp turns.  Really the best way is spaghetti with gradual bends.