I think about this all the time. I'm a little confused by your statement "It became quickly apparent that the set came first (either in idea or in execution) and the blocking came later... at the expense of the set."  I think the set has to come before the blocking. I would not want to have to design a set around the blocking. that would be a setup for failure.

To me a set should always be interesting. a boring set doesn't add anything to a show and can even detract. That's not to say you can't do a very minimalist approach; minimalism is a very appropriate design choice for some shows.

I too have designed and built things that i wish the director/actors would use more than once (or at all). Sometimes I will tastefully suggest to the director that he may have missed what I was envisioning and I want to share it with him. However I try very hard to not complain or feel diminished if he rejects my suggestion. (at least not to him or the actors. my girlfriend hears some complaining sometimes.)

What's particularly frustrating to me is when i have a great design idea which gets rejected in the initial stages and it becomes absolutely clear to me during the rehearsal process that I was completely right and it would have worked perfectly my way and what we settled on is a pale second. Usually though that was a failure on my part to explain or present my idea well.

Ultimately the blocking choices fall to the director, as we all know. How to keep the set from "taking over" is a challenge sometimes, but i think it is lessened significantly by good communication through the entire design/build/rehearsal process.

To further (over)clarify, most shows start with the script and rough blocking needs; ie, need a door into the kitchen and a place to call the bedroom. They then design a set that meets these needs and more, and specific blocking happens from there.

Sometimes the director or set designer skip the first step and either block with no concept of the finished set or build a set with no concept of how the actors will actually use it. In either case, blocking then must change to accommodate the set, often resulting in awkward movement on stage.

And then there is the third situation, where director and set designer come up a novel set design and purposefully block the actors into utilizing that set every possible moment. This often results in arbitrary and confusing blocking.

Right now I am working with a director who had her entire set design done in her head before the first production meeting (she does not have the "experice, knowledge, or ability").  There was no room for discussion in her mind though.  So when does "everything should be up to the director" become too much?