Bill,
I would be glad to try to reply, but it is a broad question, and the answer would be "every project is different".
First of all, everything Tim Weiman says is absolutely true, and would create an ideal working environment. Usually, by the time an architect is hired, the owner has a good idea of what he may want to do, and why he wanted him/her in the first place. Along the way, many little issues arise as you try to balance the design needs of the owner, future customers, views from surrounding housing, mainteance practicality, etc.
Any modern design school will teach the "zen" approach to design - first, strip yourself of all ego. Of course, that doesn't really happen, but in reality, you should design for the end user, and for the owner's design program, but not yourself. One on hand, many at GCA would vomit at that suggestion, feeling the architect should be completely free to express himself. On the other hand, it sure is a good starting point as a method to keep yourself from "standard formula design," which we all hate as well.
I don't know how that applies to buildings, but in golf, I know if I am commissioned to do a muni, I go in with a more pliant attitude regarding the owner's wishes. If he is conservative, I am conservative, in trying to stay within his design parameters for difficulty, ease of maintenance, etc.
If I am asked to do a resort course with national/regional attraction attraction qualities, I may push more. If the owner is afraid to get bold, I would (tactfully) make as many arguments in favor of my design ideas as I could. The funny thing is, these types of owners usually let you have more free hand, and/or are more inclined to go with your suggestions.
Smaller projects, including remodels, are usually more closely scrutinized, if for no other reason that the existing owner/membership knows what the course used to look like!
In fact, its not just the owner who sets the tone for the project. First, he is not usually an individual. He is usually a government agency or corporation. A project manager is appointed. He relies on consultants of many kinds, some of whom have come together quite randomly. He may have a superintendent and or pro, feasibility consultants, etc. If all are conservative, it's hard to push a flashy idea by them.
That would call for some real slight of hand. Of course, that would be the topic of another thread!