I think you missed the co-equal part of the argument.
I don't believe I missed that at all. The three branches are not independent, they are linked by the US Constitution. They do not operate by different constitutions.
Delay is correct, Congress controls the extent of the judiciary, how far it may reach into the lives of the citizenry.
To say that the branches are 'equal' is not to say for example that the Executive branch need not respond to Congressional inquiries, need not show up under subpoena, need not respond to impeachment proceedings and verdicts.
To say that the Judicial branch is 'equal' is not to say that judges need not respond to Congressional subpoenas, need not consider laws passed by Congress, need not abide by the budgetary allocations set by Congress.
We have seen Congress cede its power to the other branches. It no longer 'declares' war, it no longer intercedes in bringing about floor votes over innocuous debate by a minority and it no longer affirms the proper layout of the judiciary.
Madison vs. Marbury has been left unchallenged not because the issues it embodies are complete and unequivocal, but because the conduct of the courts until recently in the last decade and a half have been self-restrained in a low profile state. All that is changing presently. Although Madison vs. Marbury will not likely be resurrected, judges will find themselves increasingly in contempt with the other branches until they relearn the wisdom and practicality of self-restraint.