I agree with Brian, the choppiness is much more likely to have to do with excessive bitrate than the format at hand. For reference, youtube uses a 2Mbps bitrate for the 1080p VP9 videos they serve. I'd recommend trying to compressing the original VP9 video at that bitrate to see if the choppiness goes away.
If that solves the problem, I think it's an indication that we should transcode videos down to a lower bitrate when the original bitrate is too high, even when the format is playable as-is.
As an anecdote, in ye olde times of learning DVD production at university, we were shown statistics about how real dvd players handled bitrate in the wild and it turns out that you had to be extremely conservative about both the average bitrate of your video and the maximum peak bitrate (when using variable bitrate), otherwise playback could be choppy on consumer DVD players. I can't remember the values, but they were very far from the theoretical maximum of the DVD specification. As much as it sucks to see the quality loss due to the extra compression required to abide to very conservative bitrates as the publisher of the video, it's what made the difference between the video being playable at all by people or not. If it's choppy for them, they're definitely not going to watch the whole thing.