My first question is what the aspect ratio should be. I'm guessing you are resizing to 720x480 (anamorphic 16x9), but it's a bit hard to tell if that's right from the sample.

The MOST important question is what are you using for your resize filter? If you are using something like bilinear you are getting aliasing artifacts from that (stairstepping along diagonal lines). Try the Lanczos3 resizer (it's the same as avisynth's Lanczos4resize), it produces a much cleaner result.

Finally, what sharpening filter are you using and why? I would never add a sharpen filter to this clip, it is absolutely beautiful. You are downscaling HD, you can't get much more detail into it than that. It will only cause more stairstepping and ringing artifacts.

Really just open it in VDubMod, add a resize filter (Lanczos3), 720x480 and frameserve right to your encoder. Don't do anything else and I think you'll like your results better.