Jellyfin did some work on integrating the Skip Intros plugin a lot better, AFAIK you just have to enable it once on your server and then once in the settings of all Jellyfin web players.

As for apps, there are some good native third party apps which I mentioned here.

Was this with the first party Jellyfin app or with Swiftfin?

If it was with the first party app, I’d definitely recommend giving Swiftfin a try.

Jellyfin has native apps for Android, Android TV and iOS.

Does Plex offer native apps (that aren’t just stripped down browsers) for more platforms?