MediaCoder

If you want to alter luma - brightness or contrast, you can. Whether there is a specific difference in the levels for HD and SD, that is listed somewhere, I don't know.

If you want to alter chroma - R,G or B separately with MC, you can't. It doesn't work.

If I recall, if the frame rate is variable and you set a specific rate, (converting from rmvb or some foul container ), it will force more constant frame rate.

With no harddup and VBR, the rate may truly stay VBR as no extra frames will be added to keep it constant.

Set the AR as well as resizing or set PAR=VGA11 so the header knows not to copy the AR from the previous file.

If it doesn't need the bits, it won't use them.

If you just want a smaller container, no worries. I have not found really good settings for xvid to x264 that don't look a bit fuzzy in the shadows, but I have only done a couple with mencoder. Increasing the resolution won't make it any sharper, though. If it already has the proper AR with VGA11, w...

Avis are neither PAL nor NTSC; they just have different frame rates. If your setup plays 23.976fps and 29.970fps avis, there is no reason it should not play 25fps. PAL and NTSC are dvd labels. Since you want to recode to another codec/container, for some reason, that also has no PAL/NTSC distinction...

Actually the frame rate can fluctuate. Try setting the frame rate rather than just using original or no setting.

If you mean bit rate, that is different.

It probably is not multiplexed correctly. Try AVIMux_Gui

Also if you are just copying the aac audio, which may be 6 channel, try converting to mp3 or doing the audio separately and then muxing.

There is the high probability that the first one has duplicate or blended frames, because the original will either be 23.976, 24 or 25 fps.
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The 25fps video will play more smoothly unless it is something like a US cartoon will tons of blending.