^Like it or not, it's his movie, and it should be his decision. Sure, you can say that the studio should be entitled to override the decisions of a director whose work you're dissatisfied with, but the flipside of that is that they're entitled to override the decisions of directors whose work you do like. The sad fact is that studios already do routinely override directors' creative vision, and the result is detrimental over 90% of the time.
Indeed, that's why we get directors' cuts on DVD in the first place: because in America, it's the studio rather than the director that gets the final cut on a film, and so many movies reach theaters in a form their directors are dissatisfied with. So there's the flaw in your logic: the version of NEM that hit theaters was the one Paramount was happy with, so they'd have no incentive to change it.
Personally, I think we've gotten absurdly spoiled -- in just a few short years since special cuts started coming out on DVD, we've come to think of them as an entitlement rather than a bonus. Nobody should have to justify the decision not to do one, because it's not a requirement.