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>The resulting video is very nearly the same file size
That doesn't seem right.
Pixel resolution does not have as much influence on the final file size as one might think. For example, if you export a video at 320x240 and another at 640x480, the latter will not be twice as large in bytes as the first, in fact they will both be quite close in file size. So that is not something to worry about. What people should always consider when compressing for the web is to make sure the video's resolution is divisible by 16, 8, or 4. If the resolution does not fit this criteria, then it can contribute to choppy playback by the viewers system.
The high-res version of the "Gallows" video was choppy on my end as well, but that is more than likely due to the fact that the codec used is avc1 and the resolution is 1920x1080.
You are right about resizing the video to the players dimensions. This will without a doubt help with decoding of the video on the local system, as well as speedup the progressive download playback. I had no problems playing back the "sized-correctly" version from your website.
As far as color reproduction goes, I looked at the two videos in VLC side by side at roughly the same resolution and I could not see any noticeable difference between the two. Detail was a little softer in the "sized correctly" version, but that is par for the course when resizing video and compressing for the web. The higher resolution version has more pixels to display than the smaller one, hence the difference in detail between the two. The additional data in the smaller version was thrown out when you resized and exported the video.
Read the following learning guide from Adobe for a little refresher:
Brainless, sorry, can't write your name without laughing.
If you kept the data rate the same when exporting, the window dimensions will be smaller but the file size just as big. I'm not sure you have that option (don't have CS4), but the file size being the same makes me wonder.