Bloodstained Ritual of the Night/Curse of the Moon (Castlevania, both classic and Metroidvania style)
Eiyuden Chronicle: Hundred Heroes (Suikoden)
Penny Blood (Shadow Hearts)
Armed Fantasia (Wild Arms)

Heeey! Park Boy: Chibi Robo
24 Killers: Moon Remix RPG/Early Love-de-lic
Yooka-Laylee: Banjo-Kazooie
Yooka-Laylee and the Impossible Lair: Donkey Kong Country
Kaze and the Wild Masks: Donkey Kong Country
Lunistice: Early 3D Sonic
Chasing the Unseen: Shadow of the Colossus

Also, I didn't list anything due to sheer volume, but there are a ton of Pokemon clones and Earthbound inspired indie RPGs on the market now, not sure if you'd want to include those. Same goes for all the Harvest Moon inspired indie titles (aside from the obvious one in Stardew Valley)

Oddity is a spiritual successor to Earthbound/Mother that originally was titled Mother 4, it's not our yet but I think it would still count

Fight'N Rage (Streets of Rage, this was before SOR4)
Spark the Electric Jester 2 (Sonic Adventure)
Dusk (Quake)
Sea of Stars (Chrono Trigger)
Axiom Verge (Metroid, before Metroid Dread)
20XX (Mega Man X)
Tormented Souls (Classic Resident Evil)

These are just the ones I know people generally like.

Not sure this fully applies since the Sonic series seems to be sorta back in the same vein with Sonic Frontiers specifically but the Spark the Electric Jester series feel like a successor to the Sonic Adventure games

Wargroove (Advance Wars, before the remakes)
Freedom Planet (Classic Sonic, before Sonic Mania)
Triangle Strategy (Final Fantasy Tactics)

Fur Squadron (Star Fox 64)

Just remembered the upcoming indie game Demonschool looks like a spiritual successor to persona 1/2 and other early tactics/strategy games

Tunic (Pre-Botw Zelda) maybe?

@Drax Yeah, unless the inspiration is pretty explicit, I'd rather not count Earthbound/Pokemon-likes. Especially Pokemon, that game series is going to keep going forever, I doubt its core mechanics are gonna change anytime soon. Same with Stardew Valley, games like Harvest Moon Story of Seasons still existed at the time, and continue to exist to this day. Not exactly what I'm looking for.

Also you reminded me that Heeey! Park Boy exists, and that brightened my day a little bit.

I was looking for a list like this!

@Monado_Lad

Tunic fundamentally is closer to a Souls game; it’s just wearing the skin of classic Zelda. Honestly Cross Code is closer to a take on classic Zelda since that game is full of dungeons with puzzles contrasted by an overworld; Tunic’s levels are mostly combat focused which I guess is closer to Zelda 1 than any other entry

Buck Up and Drive to Outrun?

idk if this fully applies but sea of stars looks like a spiritual successor to chrono trigger/mana games

@SunlitSonata good point, Tunic is just a Zelda game in my brain, the stylistic similarities stuck with me more than the actual gameplay I guess.

Updated with most suggestions.

LunarLux (Mega Man Battle Network/Mario & Luigi Series)
PsiloSybil (Crash Bandicoot PSX games)

I don't know much about the Rythm Heaven games, but Bits & Bops looks like an spiritual successor

please disregard every line after this one
Natural Selection 1/2, Unvanquished (Alien vs Predator 2000? it's the one with asymmetrical multiplayer)
Midair 1/2 (Tribes 2, Ascend, not sure if the first one was an inspiration)
Neverball, Rolled Out (Super Monkey Ball)
Gnomoria (graphical Dwarf Fortress, shoutout to when Minecraft and Towns also tried that to lesser results)
Starbound (ex Terraria dev :^) )
Wreckfest (Flatout)
Toxikk (Unreal Tournament 2004)
Hedgewars (Worms Armageddon)
Reflex/there's more but i cant remember their names exactly (Quake 3 CPMA mod)
BeamNG (Rigs of Rods)

Donut Dodo (Pac-Man and Donkey Kong)