I actually use both apps, I find Organic Maps a lot nicer for looking at a map and navigating by foot or bike, and Magic Earth seems to pick more sensible car routes some times. Also the live traffic data makes it more fitting for car navigation (Organic Maps doesn't have traffic data).
eco_game
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?
I can highly recommend Magic Earth as a Google Maps alternative (also available for Android). It uses OSM data and has some traffic info. It's not as good as Google, but it's the closest I've found so far.
The newer Sony Xperias sound like a good fit for you. I haven't used one myself, but they're pretty decent from what I can gather.
Also it seems as if Sony is the only phone manufacturer shipping flagships with headphone jacks and SD card slots.
On another note, I highly recommend the GSMarena Phone Finder for getting a general selection of phones that have the features you care about.
I find the Jellyfin webapp a pretty bad experience on mobile, compared to FinDroid.
I really like the webapp on my LG webOS TV (especially good with the Magic Remote) though.
So I guess it kind of depends on the platform.