I stand on my position that the problem with Other M is not as much the game, but WHEN it happened. Put it anywhere between Zero Mission and Super, and ignore the Prime games like the creator does, and you have a solid game. A Tale of a Samus that fought her demons but sees that she can never get free. (But it makes it make more sense if the game is before 2, so that there is the "ok, cloning Metroids was a bad idea, so lets kill them all" type of deal.)
But then again, it throws a curve ball in character development even as it stands. And I think the issue people have is not with the character development, but how the character was developed. Maybe Other M is really the moment Samus realized there would be no victory against Ridley. I mean, she just blew up the god damned planet he was on, after sending him to melt in a pit of Lava, and destroying everyone that would be reviving him, and he's back to life.
I mean, maybe after Super, Samus had decided to retire, put a down payment on a nice cottage in the Retired Bounty Hunter Nebula, was was on her way to finally rest after years of dealing with her childhood fears and facing the Pirates. And damned if Ridley isn't back. And not only that but she had him at her mercy before and did not shoot him. There's a lot more to Other M that isn't outright stated in the game but that makes a whole lot of sense. Hell, people have been dying left and right around Samus, and these people were her friends in the federation. In other games, Samus was pretty much alone, and she never had that rapport with other characters around. So you're telling me that having your friends die on you, and a monster you killed twice (again, Primes are not cannon), come back to kill you, and not only that, you failed to kill him when you had a chance.
Tell me that isn't the least bit traumatizing.
(Also, I find that when people mention they hate the character development, they mean Samus freezing against Ridley. And as for humoring Adam and his directives, it wasn't a serious mission at first, also Adam knew that giving Samus free range would make her quite pissed at the federation, and also there was an assassin on board, and Adam had no way of knowing if it was Samus or not, so granting her with the full use of her weapons would have been making her unstoppable.)