The only reason the video is 360p is because he didn't upconvert it or scale it, so it uploaded at the NDS' native of 256x192 per screen (256x384.) I'm pretty sure Desmume's internal recorder can scale.
Use a better codec than Microsoft Video. Encode it with H.264 after you record it (FFmpeg is great for this) so it can have exceptionally great quality with a low size.
Koopa tends to know what he's talking about, and definitely knows more on the subject than me so I would definitely try this
