This is a few months old but I thought I would add what I gathered from my own experiences with Youtube.
Youtube seems to transcode everything you send them, even if you follow their recommended encoding.
It takes them time to transcode it all, starting with the lower resolution versions (240, 360 and 480). You need to wait for the HD versions to finish processing, and this can take quite a while (even if youtube says it has finished…)
Make sure you give it plenty of time to sort itself out and make sure you’re watching the HD version instead of a 480p version.
We upload in the best quality we can (usually 1080p25), and provided you give it time to process everything it usually looks pretty good.
Incidentally, we noticed youtube pushed the red in some of our videos. We ended up having to produce two versions of content, one version would have the red pulled out by about 3% to counter the youtube push. Never worked out why that happened, but doesn’t seem to apply to all our content.