Heyo! I used to run into this situation pretty often, especially while in film school, but as I've grown professionally I've realized that more often than not the problem is not the director's inexperience / poor opinion / limited budget etc., but my own failure to totally grok the experience they're trying to craft.

Here's the important thing: Ultimately, it's the director's film, and what they think sounds right is much more important than what you think sounds right. They're the lead creative force behind the project, and if they're making uninteresting or cliched sound decisions, you have to either re-evaluate your understanding of what this movie is supposed to be, or you have to convince the director of why your particular decisions are the right ones for the movie they're making.

What doesn't work is just saying something's a bad decision, or doesn't sound good, or isn't the way things are done. Every project is different, and the director knows that just because something is "wrong" for other projects doesn't make it wrong for this one. You have to come at it from their perspective, and really focus on why a particular decision doesn't work for this particular movie.

Finally, it's crucial that you and the director be making the same movie. Disagreements are healthy as long as they ultimately either enlighten you with an aspect of the director's vision you hadn't considered, or enlighten the director with a way to achieve that vision they hadn't considered. If you're having a lot of disagreements, then before becoming frustrated with the director you should think long and hard about what it is that you're not getting about their vision. And if even after that you think the director's wrong, be prepared with rationales specific to this film, this audience, etc.

But I'd recommend absolutely stating your opinions and being prepared to learn something. If you don't voice your disagreements, the collaboration is doomed because you're idea of what this movie should be (sound like) don't match the client's.

Sorry for the long post. My 2cents :-D

Good luck!

You sort of answered your own question.

It all really depends on how questionable the situation is, but if there's one thing to remember if you already agreed to do the job is that ultimately it's about the Directors vision, not yours.

You might want to provide alternate and informed options so they can hopefully choose wisely. Don't give them more than two alternates though, otherwise you may give them option anxiety.

You really just have to learn that sometimes your material might get deleted or replaced and roll with it. It's happened to the best of us and will undoubtedly happen to all of us in our lifetime/careers.

Give them examples and feed them ideas and reasons why it will work better than what they want. A lot of the times directors don't have a clue about sound. If you're on the job from pre-production show how much you know about sound by requesting specific things from the recordist (unless you're doing it yourself) and make your position and opinion an important one from the start.

director calls the shots ;)

The director is always right. Our job is to be invisible and support everyone else.

Here's a great article on something sort of similar from Lifehacker it was posted just a few days ago.

I believe that it is the designer's job to help express the director's (or creative lead's in the case of games) vision of the show, but if you have some experience, then you probably have some insights that no one else has and IT IS YOUR JOB to present them (hopefully in a manner that isn't confrontational or egocentric).

When my input is not taken then i fall back on advice I was given a long time ago by an experienced mixer at the old Todd AO East. He said that you have to know what hills are worth dying on. A small sound during an inconsequential scene is probably not the place to dig your heels in.