I'm going to run the gauntlet here (oh, and Gauntlet is on the list!). Get ready to cry everyone...

King's Quest
Chrono (seriously Square, this is how you print money)
No One Lives Forever (the rights mess is just an unbelievable example of how we need IP legal reform)
MegaMan X (seriously Capcom, this is how you print money)
Adventure Island
Secret of Evermore
Hotel Dusk
Rogue Squadron (probably best after Kathleen Kennedy)
Punch Out
Breath of Fire
F-Zero
Donkey Kong Country
Battletoads, Banjo Kazooie, Perfect Dark (or really, any classic Rare series)
Skies of Arcadia
Space Channel 5
Kid Icarus
StarTropics
The Adventures of Lolo
The Last Story
Fortune Street
Metroid Prime (there, I said it)
CrossCode
Golden Sun

Still on GOG: https://www.gog.com/en/game/leisure_suit_larry (other games in the series as well)

Oh, oh, the dangers of sexuality. While showing violence is A-OK, obviously. We came a long way from Make Love, not War. No wonder the US is so fucked up. Violence is normalized, sexuality demonized.

Since Nintendo as the new owner revisited Another Code (with a remake of both entries) I got some hope for this one.

Mario. We've seen the last of him I'm afraid. He had a good run.

Chrono Trigger is probably being remade/remastered, but yeah the series is probably done.

Suikoden Star Leap just released in Japan for mobile and PC. It seems to be a great game and is faithful to the originals (S1/2 art and gameplay style, charming, good story, canon) but with some of the standard f2p caveats. I think the odds are decent that a console Suikoden 6 is coming at some point in the future.

Capcom keeps bringing old games back, so I imagine Breath of Fire will return if maybe briefly and as a low budget spinoff.

Legend of Dragoon and Xenogears aren't returning. But neither is a "franchise". Xenogears may get remade/remastered though.

No One Lives Forever comes to mind, due to being in legal limbo between Warner Bros, Microsoft and Disney.

Well that's a fitting name.

The two last ones that were made in the Kickstarter era after Sierra went under, Wet Dreams don't dry and Wet Dreams Dry twice, are sadly also missing there. It's those to that are getting delisted everywhere for unknown reasons, though probably has something to do with the license (probably only had the rights for Larry for a specific timeframe).

Tragically realistic.