Watched a couple more episodes, noticed some more things:

Seems to be a high-pitched whine in the audio, maybe due to YouTube compression?
“Dark Awakening” has a glitch in the video at about 10:00, also uses the “Return of Optimus Prime” narration at the end
Still plenty of film dirt and scratches visible, some grain in lighter colors as well
edge enhancement on lines seems a bit more pronounced due to the upscaling

Still though, probably the best way to watch these officially. I do hope a new film scan is done for Blu-ray someday, but we probably shouldn’t get our hopes up…