I don't like Fallout 3's storyline and most of its characters and I've made this clear on multiple occasions. However, I find some of potential in creating alternative readings of the story, as poor as it is. One of my favourites is treating http://fallout.gamepedia.com/James as a psychopath, not in the figurative, but in the literal sense. Let's start with the http://en.wikipedia.org/wiki/Psychopathy:

Fancy, but meets my requirements. Let me demonstrate this further by including each of the three indicators of a psychopathic personality. As the original article points out, these do not apply to every case and manifest differently depending on the individual.

In many contexts, this personality trait is considered a positive thing. However, in James it manifests in a number of ways that are not as... Positive as this trait can suggest. Let's enumerate some of them:

1. James leaves the Vault when he becomes convinced that he has solved the problem with Project Purity. This is a bold move, far more than anyone in the Vault has ever thought to do, including challenging the Overseer's authority. Unfortunately, this causes death, upheaval, and endangers his child, whom he declares he loves.
2. He heads to Vault 112 without caring for the fact that it's inhabited by an insane overseer who's more than two centuries old. As he points out in his holotapes, he *knew* who Braun is.
3. James effectively forces the Rivet City team to travel to a super mutant infested locale on his demand. He doesn't care about the dangers to them or himself. In fact, we can observe his confidence and assertiveness in each conversation and interaction he has with people. Assertive and confident, but mostly he appears forceful. The way he manipulates Li into doing his bidding is a good example.
   

Oh yes, one of the two primary crimes. James is impulsive and fails to plan ahead. To wit:

1. The moment Catherine dies, he loses interest in Project Purity and abandons it. He heads for Vault 101 without caring for the project or its participants.
2. Inside the Vault, he shows some control, but the moment he renews interest in Project Purity, he starts stealing equipment and technology to run his tests, bringing Jonas in and effectively condemning him to death.
3. As pointed out above, he decides to leave the Vault on a whim. Not telling even his child, officially so that they can stay "safe" - with an egotistic, violent Overseer with a personal goon squad. Funny how James, with all his medical knowledge, failed to realize this.
4. James' suicide is not noble. It's entirely to spite Autumn and the Enclave, so that they do not control the Purifier. Think it's rage directed at the fact Autumn just shot someone? Re-examine it from this perspective. James had nothing to gain from destroying the Purifier and robs the wasteland of the largest clean water source, just because he isn't the boss anymore.
   

My "favourite" element. Throughout the game he shows that. Let's start with a few examples:

1. El Dubya's birth. Normally, a medical doctor would attend to the woman with the torn, gaping [censored] and possibly internal bleeding: Post-natal Catherine. But no, his first reaction is to ignore Catherine and start fiddling with the new toy he has. Poor Catherine then goes into cardiac arrest. Maybe if he didn't screw around with the genetic projection and had Li actually attend to Catherine, she would've lived. Maybe not. But it struck me as horrifying.
2. Treats El Dubya as a pet. It's subtle, but I found it interesting that the player is forced to follow James in the chargen sequence like an obedient dog, a terrier. Ever noticed how he has the kid walk barefoot on the cold Vault floor, following him like a puppy?
3. The aforementioned Vault escape is an excellent example of how he defies authority and lacks empathy. Anyone with half a brain would figure out that the bat[censored] insane Overseer would blow his lid and start wrecking stuff. James decided to escape regardless, even though he was leaving his child and friend behind to be killed.
4. The way he travels to the Memorial and through DC would fit into the destructive excitement seeking element. After all, who does it with just a jumpsuit and .32 pistol?
5. Impulsiveness and demand for instant gratification also *define* his behavior. He has no interest in PP anymore? Off to Vault 101. Hey, experiments work? Off I go, kid and Jonas can die. Li doesn't want to cooperate? Manipulate her into restarting a 20 year old, derelict project. Can't convince the Enclave to leave? Oh, I guess I'll kill myself.
6. Lack of empathy also extends to his reactions. Blow up Megaton and what he will do? Deliver a stilted monologue about how "appalled" he is, but that he still "loves" El Dubya. If you treat James as a psychopath, it explains a lot: He doesn't understand empathy, but he knows killing an entire town with a nuke is considered bad, so he tries to formulate a response in a way he thinks people would react. But he doesn't have the capacity to understand human reactions to it - or indeed treat the act as evil.
7. Finally, the motivation for suicide. It's spite. He could work with the Enclave to subvert their goals, negotiate with Autumn (in a way that isn't basically telling him to go [censored] himself with a rusty rake), or hell, anything that doesn't involve killing everyone off and dooming his kid to fighting Enclave mooks for the rest of the game. But no, when he realizes he won't have his candy, he kills himself, Autumn, and everyone in the control room.

And that's just what I have off the top of my head. For reference, here's the dialogue file. From where I stand, James appears as a manipulative, heartless psychopath who does everything on a whim. How does he appear to you?

Interesting interpretation, but as we know this is only possible because the MQ was basically written just to get it over with, and because they had to give Liam Neeson as little dialogue as possible - of course they could've avoided that situation by hiring a VA that doesn't cost half the game's budget. He was clearly meant as the loving father - the people doing the manipulation were the writers who thought they could make the MQ appear deep and well-written by introducing such a character.

The only thing I disagree with is prolly that James not noticing Catherine's extensive bleeding is not caring about it. Firstly, I think aside from the gene projection the place was pretty much third world condition. Secondly, there was Dr Li, she didn't notice either and she's no psycho.

Anyhow, a favorite theory of mine, somewhat related to this: the LW is meant to be a girl who has serious daddy issues in the sense that she misses her father and expresses these feelings in a childish manner ("I miss him so much" even Three Dog is like wtf) and apparently is willing to kill her way through the CW to find him.