My Top 2:
- Batbarian: Testament of the Primordials
- Phoenotopia: Awakening (fair to say it's more a Zelda 2-like but I always had the feeling of playing a metroidvania and it's described as one basically everywhere)
Other favorites (unsorted):
- The Aquatic Adventure of the Last Human
- The Mummy Demastered
- Yoku's Island Express
- Monster Boy & The Cursed Kingdom
- Cathedral
- Hollow Knight
- Control (one of those 3D metroidvanias you asked about)
- Pitfall: The Lost Expedition aka Pitfall: The Big Journey (3D)
- Castlevania: Symphony of the Night/Aria of Sorrow/Dawn of Sorrow/Portrait of Ruin/Order of Ecclesia
Some good & great entries, just my opinion (unsorted):
- The Messenger
- La Mulana 1&2
- Odallus: The Dark Call (Lvl select with necessary backtracking)
- Ori & The Blind Forest
- Ori & The Will of Wisps
- Nightmare Boy (people love it or hate it, I think it's chaotic fun)
- Kunai
- Touhou Luna Nights
- Elliot Quest (Zelda 2-like)
- Axiom Verge
- Finding Teddy 2 aka Chronicles of Teddy: Harmony In Exodus (no need to play the first one, it's self contained, first one is a Point&Click adventure)
- Owlboy
- 3000th Duel
- Aggelos
- Mystik Belle
- Chasm
- Momodora: Reverie Under The Moonlight
- Minoria
- Guacamelee 1&2
- Shantae 2&3
- Escape from Tethys
- Castlevania: Circle of the Moon/Harmony of Dissonance
- Alwa's Awakening & Legacy
- Willy Jetman: Astromonkey's Revenge
- Timespinner
- Bookbound Brigade (it took me a second attempt to really appreciate this game after some hours and movement upgrades)
- The Witch and the 66 Mushrooms (mini mv)
- Gato Roboto (mini mv)
- Inexistence: Rebirth (mini mv)
Don't care if it's a big epic or just a smaller scale mini metroidvania. It's my favorite genre and I rate every title I've played into masterpiece, great & good+ which land on this list for recommendations and good-, meh & avoid won't land on this list. Everybody has different taste for sure and that's good so that are just my personal twisted opinions. XD For example I'm not a big fan of Blasphemous which a lot of people tend to love (pixelart and OST is amazing though) .

On my toplay-list or what I'm waiting for release (on consoles):
- Treasures of the Aegean
- Heart Forth Alicia
- Dogworld
- Deaths Gambit (Afterlife upgrade)
- Aeterna Noctis
- FIST: Forged In Shadow Torch
- Transmute
- The Siege and the Sandfox
- Environmental Station Alpha
- Ender Lilies
- Gestalt: Steam and Cinder
- Faeland
- Lost Ruins
- Fearmonium
- Plague Huntress
- Winter Belle
- Lore Finder
- The Last Faith
- Axiom Verge 2
- Metroid series
- Astalon: Tears of the Earth
- Monster Sanctuary
- Record of Lodoss War: Deedlit in Wonder Labyrinth
- MindSeize
- Curse of the Sea Rats
- Bloodstained: Ritual of the Night
- Hollow Knight Silksong
- Goodboy Galaxy
- Sheepo
- Souldiers
- Demoniaca