I have multiple characters but I'm seriously considering just abandoning most of them altogether due to most of the differences aka companions are now pretty much gone.

As far as I'm aware the only companions with ongoing stories are:

-Kira/Scourge

-Lana

-Theron

Apart from new characters that have showed up in more recent updates. Do you think it's safe to just focus on an e.g. Jedi Knight run and a Sith Warrior run now? Or am I forgetting a companion who hasn't been reintroduced?

It's a common complaint. Companions who don't show up in Fallen Empire/Eternal Throne only appear in the Alerts and then they're done. Companions who don't appear in Alerts arrive in stories after Fallen Empire - Doc, Nadia, Raina, Quinn, Elara, Kira, Scourge. Zenith was the last hold out finally having made an appearance after the Enclave story. Don't expect much. Gault makes an appearance when you go to Meksha. Torian has a cameo in Spirit of Vengeance if you saved him in Fallen Empire.

There are theories and realities why the Companions were abandoned, but there's always hope a new story will bring one or two back to prominence for a little bit.

There's also the meta-game reality that the game and story couldn't possibly continue on in perpetuity. The original Class Stories are epic in themselves. You continue on for the play of the game, but there's no harm creating a new character to replay the Class Stories to enjoy them again, try a few different dialogue choices for variety and see what happens, and don't continue on when the story completes. You have your Star Wars story. Enjoy that.