Used both at one time, Skytube didn’t work as well as newpipe on my devices. Maybe that has changed now since some time has passed. It doesn’t seem to be updated much on fdroid with the last update being 3 months ago and didn’t update for 5 before that.
It wasn’t a bit fan of the video interface, it felt like I was watching YouTube on the mobile site.
The big thing was being able to download the video and audio. Skytube only allows video downloads. If I want offline music, I can only use Newpipe. And Newpipe let’s me decide which quality and file I want per download. It also allows downloads from SoundCloud, media.ccc.de, framatube and Bandcamp.
From what I understand, Skytube is now using Newpipe’s api for the back-end by default, so take that as you will.