Perils of the Writer: Inner Motivation and Inner Conflict

Stories need to be driven by choices and consequences.  The consequences are the external stuff, but choices are internal.
And nothing kills a story's investment like a lack of choices.
Part the key, I think, is making sure the choices your characters make are both A. a legitimate choice between two or more options and B. a logical expression of the character.
The first part of that comes from not making it seem like the plot is just dragging the character by the nose.  If there aren't real choices, then it's old-school video-game plotting.  The character just moves forward from scene to scene, with events dictated to them, rather than having any real impact on the events.
The second part is a counterbalance to that, in that if you're writing the character correctly, it's clear that the choice they make is the only one they really are capable of making.
It's not unlike the predestination/free will argument.  You can make any choice you want, but this is the choice that you are going to make, because that's who you are.
Now, choices tend to fall into three categories: Need To Do, Want To Do and Ought To Do.  Internal conflict sparks from those three things being out of alignment.  Need To Do are the pure survival-necessity choices.  Lizard-brain reaction. "I'm running out of air-- I need to get to the surface!"  "This guy's trying to kill me and I can't get out-- I need to fight back!"  Want To Do are emotional choices-- rational thought is involved, but the emotion behind the thoughts are the drivers.  "My friend's in trouble-- I want to help them!" "That's the guy who killed my father-- I want to kill him!"  Ought To Do are the higher-thinking choices, the moral choices.  "This person is trying to seduce me away from the mission-- I ought to walk away from them."  "Killing him now will put my friends at risk-- I ought to let him walk away."
Now, often the "Ought To" choice is the objective "best" choice... but that doesn't mean it will be the right choice for the character to make.  In fact, good storytelling often comes from characters making the wrong choice, objectively, but the right choice for the character.  That's key: don't have a character make a stupid choice just so the plot can keep moving.
Unless it's right for the character to do something stupid.
See you all in the word mines.