Sirren, your solution will make pretty much the same level of quality as the solution I offered, except that you can't perform batch operations with it. Not only that, but depending on what you're using to select by color, it'll still leave artifacts or take out chunks of the character if you try to compensate for those artifacts.
Fallout2 doesn't support semitransparent pixels, correct? Therefore rendering a larger size, cutting the image out and then resizing back down won't work since you'd have to resize back down without any interpolation (no cubic/lanczos/whatever) in order to not have antialiased edges. This would in effect downgrade the quality of the inner details and make it less distinguishable. It probably worked for you because trees don't require specific detailing to look alright when it's low-res, not to mention they're less dynamic.
Simple way to render an alpha channel with shadows is to make your own alpha channel. After you've rendered all the rgb frames, make a copy of the anim8or file(s), and give your objects a stark black material with no specular. Make a new object and add a plane to that, assigning a material with black ambience and white diffuse (value of 2 or 3 for the diffuse). In the scene, set up your single light (to 100% dark raytraced shadows) if it's not already set, add the plane object to it with only receiving shadows, whereas the character object casts and receives, then set the scene background to pure white as well. Render without antialiasing. I've prepared an example for you:
Example file (right click and save link/target as...)RGB
Alpha:
Combined
There are batch image processing programs out there such as
ImageMagick that will allow you to process all the frames at once via some simple scripting, making it a breeze to handle even thousands of frames automatically.
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