Wow, Helm, that was... in-depth. Thank you.

It's only (very) recently that I've started to look at my understanding of anatomy a little more seriously. I have a basic grasp of how it all lays out; good enough that it's usually passable in idle poses, and in deformed, stylized characters, but poor enough that it all falls apart when I actually try to put it to work (as you can tell by the totally phoned in gun arm ,etc.), which I took as all the more reason to steer clear of over-deformation. I've been trying to avoid of pixelling in the interim, but my attention span is pretty deplorable.

I like mostly everything you did in this edit, and it'll most definitely be helpful to say the least. That said, I might neglect this piece for a bit and go back to working on the basics.

You're absolutely right, Ryona, his feet are tiny. I've been trying to strike a balance between balance between the super long hooves of, say, the animated version, and something a little more human (though at the moment, I think I'm a far cry from either). It is something I've been thinking about, though.

I was just playing around with some stuff, and this is what came of it. The main thing that bothered me was the lower body. I found the pose kind of confusing, and had a hard time telling which leg was behind which. I darkened one of the feet and the attached leg in an attempt to make it more readable. Same goes for the arm wielding the sword. Also, I changed the angle of the front-most foot based on how I read the back foot. I figured at the angle we're seeing him from, the sole of his front foot would be visible, rather than the top.

The new sword is directly modeled off of (and crappier than) Ryona's, so if you decide to rework the sword, use her edit.

Colours you can leave or take. I was just  messing around for the hell of it.

The darker colour on the sword is so close to the lighter that it's nearly invisible now. It's funny, because the darker tone you've used on the face is better in terms of contrast. You might consider reusing it on the blade (that way you'd reduce your palette size as well). It's just a thought, but you might try playing around with the rest of your palette, too. True gray tends to leave the eye a little under stimulated.

As far as an alternative to the massive sword, why not do as Ryona suggested and give him the standard katana? Stylize it, make it interesting, but keep it slim, and more.. I dunno... believably manageable. If you do want to stick with the over-sized sword, I'd say try to steer clear of the now ubiquitous buster sword look. Again though, it's your sprite, so take it where ever you like. 

I worked it over some more, tweaked some stuff. I'm thinking about taking out the muzzle flash, and the legs still bother me. I'm having a hard time taking it any further.

Heh, Reminds me more of McGruff than Sam. But good times nevertheless.

A few crits:

First and foremost, I found the outline colour distracting. It works fine in the lighter areas, but in the darker ones, the lines lose all of their weight, to the point that they essentially disappear. To that end, the darkest colour (the black used in the ear) can be used to emphasize the outlines in the shaded areas. Similarly, the original seems a bit flat overall and while  the contrast between your existing values is good, there are just too few of them. A couple of new shades added to the coat and face help to add more volume to the forms, and give a greater sense of depth. Also, your anti aliasing falls into the realm of banding, which you can find explained by Helm here: http://www.wayofthepixel.net/pixelation/index.php?topic=5556.msg66232#msg66232
I separated the feet, and moved the head maybe 1 or 2 pixels to the right, to hopefully give a better sense of balance. In the original, it looks like he's leaning a bit to the right, and it seems he should be leaning on something to keep himself upright. Finally, as a matter of personal preference, I put his ear in front of his jaw/mouth/whatever, as I thought the original read a bit funny (at first I thought he had no ears and was balding).

I like the animation, but I'd make one suggestion involving the motion blur/speed lines. Instead of using solid black speed lines, you might try just drawing a colored blurred that follows the same line of motion. Generally, I find it looks cleaner or more polished and less phoned in or however you want to describe it. I'm probably not explaining what I mean really well, so hopefully someone can pick up my slack.