Brief explanations of the different subgenres or spinoffs of the genre, featured in the family tree on the Charts page. Some of these have been around for a long time, some I've seen mentioned in Metroidvania (MV) fan communities, and others I came up with on the spot while making it. 
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When it comes to non-linearity in the overarching structure of a game, it tends to vary a lot between games even in the same series so I didn't consider it as a staple of any subgenre in particular here, but for the Platform Adventure (PA)/MV genre as a whole, partial non-linearity with some guiding of the player in the right or expected direction is the norm. See each game entry for more info on this. ​Also note that few games meet every single criteria mentioned for a subgenre.
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By Subgenre List WIP


Metroid-likes:
This is the original formula for the genre as far as the mainstream goes, so it's considered the default when categorizing each game on the site. Single, fully interconnected maze/world or close to it, platforming, an ability gating focus, some puzzles and there tends to be some backtracking to previously visited areas to progress with abilities gained over the course of the game. Little to no NPC interaction - instead there tends to be an environmental storytelling focus which grew as the Metroid series and the genre continued and evolved post-1986. Character upgrades but no exp point leveling and less focus on gear/loot. Conveys a sense of vulnerability and solitude. 
Other examples: Antiriad, Zillion, The Goonies II (sort of), Blaster Master series, Ufouria, TMNT III: Radical Rescue, System Shock, The Divide: Enemies Within, Environmental Station Alpha, Axiom Verge, Shadow Complex?, A Robot Named Fight! (sort of), Vision Soft Reset?

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Igavanias (historically Metroidvanias): 
An evolution of Metroid-likes that incorporates more RPG elements like experience point leveling, NPC interaction, shops, loot and gear customization. Basically sidescrolling ARPGs with a Metroid-like world structure and gating. They are named after the main guy behind the Metroid-like Castlevania games, Koji Igarashi, though the series first move in this direction was really Castlevania II. That game as well as the early Zelda games were his main inspirations for Symphony of the Night, a game generally considered to be the first MV in the original sense of the term (a CV game borrowing the defining elements of the Metroid games). 
Other examples: Record of Lodoss War: Deedlit in Wonder Labyrinth (more linear), Shaman King (sort of, hub map), System Shock 2 (sort of, FP view and more linear), Valdis Story (sort of), Timespinner?, Salt and Sanctuary?, Chasm?, Super Daryl Deluxe?, Aeternoblade?
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Milon's Secret Castle-likes:
Platform Adventure game with a hub area connected to sub areas world structure, generally in a hub and spokes fashion, and where the sub areas generally require some back and forth between them to progress. The hub area is also part of the same game engine as the rest of the world and generally directly connected to it. The amount and proportion of RPG elements varies and there can be one or more towns/houses, dungeons/buildings or overworld/outdoors areas but generally no clear distinction between them. 
Other examples: Legacy of the Wizard, Addams Family (NES/SMS/GG), Cyborg Hunter, ​Flashback (sort of), Dr. Franken II (minor ability gating), Shadow Man (sort of), La-Mulana (sort of - a partial hub area connects to the entrance area and otherwise inaccessible parts of some sub areas, puzzle focused)


​Zelda-likes or Wonder Boy/Monster World-likes: 
Overworld and dungeons split to the world structure, usually with self-contained dungeons that don't require revisiting at a later point to progress while the overworld is more interconnected and serves as a hub. These tend to have more RPG/Adventure elements than the average Platform Adventure game, like NPCs, towns and shops (which are also fairly common features in old school Action Adventure games, sure, however these games were generally inspired by RPGs and ARPGs).
Other examples: Knightmare II: Maze of Galious (indoors overworld), Faxanadu, Battle of Olympus, Mega Man Legends​, Tomba! (sort of; 3 dungeons, some towns and many sidequests), Mystical Ninja Starring Goemon, Brave Fencer Musashi, Darksiders II (sort of), Legacy of Kain: Soul Reaver​, Alundra 2 (also similar to Clash at Demonhead), Tomba! 2 (sort of), Beyond Good & Evil, Cave Story (sort of), Ys: Oath in Felghana (partially TD view), Batman: Arkham Asylum (sort of), Guacamelee (sort of), Ori and the Blind Forest
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Zelda II-likes or Gargoyle's Quest-likes:
Separate overworld engine similar to older RPGs like Dragon Quest, which is generally top down view. These tend to feature  RPG/Adventure elements like NPCs, towns and shops, and otherwise have the world structure of Zelda-likes. Some feature exp point leveling (Zelda II itself is unique in that the player manually distributes stat points on level up). They also tend to feature random enemy encounters. Note that the dungeons/boss areas in GQ 1-2 are generally more straightforward than in Zelda II or other Zeldas. 
Other examples: Rygar, Ax Battler, Dragon View/Super Drakkhen​, Super Adventure Island II
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Clash at Demonhead-likes, Ys III-likes or Popful Mail-likes: 
In-game areas are separated by a hub map screen where the player selects between locations to travel to rather than freely navigating an overworld with a player avatar (or if there is an avatar, it can only move between areas - not interact with the world in any other way) or moving between areas more seamlessly (generally via doors, elevators or loading screens). In Clash at Demonhead specifically, the player can initially only travel between adjacent areas on the map, and the areas represent the routes between locations rather than locations themselves unlike other games with a map screen or overworld. This method is pretty rare compared to free movement to any visited area, but was used in some similar games, and Clash at Demonhead is more of a proper Platform Adventure game than most other similar games of the time plus it's more well known and well regarded than, say, Space Hunter. 

Some games play similarly to these in that they have ability gating and backtracking, but not towns with NPCs or shops in them, and generally a single entry point per area/level. I've referenced Quackshot for these. 

Demon's Crest (basically Gargoyle's Quest 3) can also be mentioned here, which I've seen referred to as Crest-like a few times now. Compared to other Zelda II-likes that's a game where overworld movement and interaction is more limited and without battle encounters, as well as a game with some more backtracking than its prequels, so it could either be placed there or with Clash at Demonhead, or even Milon's Secret Castle depending on which you find more important - a separate engine for the hub or the backtracking. 

​Other examples: Strider (NES), G.I. Joe: The Atlantis Factor, Phantom 2040 (mission-based), Demon's Crest (streamlined overworld)​, ​Tails Adventure, Odyssey (puzzle focused), ​Front Mission: Gun Hazard, PowerSlave/Exhumed, Goemon's Great Adventure​, Alundra 2 (also similar to Zelda), Shaman King 1-2


Dizzy-likes:
A combination of Puzzle Platformer and Maze Platformer with an Adventure puzzle focus. Progression is gated mainly by inventory item-based puzzles and you tend to have a limited inventory. They tend to feature a single interconnected maze/world like Metroid, and there tends to be little to no direct combat with enemies (players are expected to avoid enemies instead). Given the lack of ability gating in most of them (?) they can be considered an outlier to the genre, but there are exceptions such as Fantastic Dizzy. 
Other examples: The Castle and Castle Excellent, Citadel 1-2, Terramex, Palace of Magic, A Boy and his Blob (NES), Shadow of the Beast 2?, Wario Land 3 (sort of)
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Horror/Survival Horror or System Shock-likes: 
Some Platform Adventure/MV games like Metroid 2, System Shock, Metroid Fusion, Shadow Man and others have enough horror elements to be considered Horror or Survival Horror hybrids. The first of these that tends to be considered a proper Surival Horror game seems to be System Shock. 


Spyro 2-likes or Banjo-likes:
Similar in structure to Milon's Secret Castle but really an offshoot of mid '90s 3D platformers, these have open-ended levels/sub areas and NPC quest givers within them as well as basic trading. These tend to also be collectathons, meaning you have to collect a relatively large amount of some generic item to unlock certain gates. 
Other examples: Ratchet & Clank 1-2, Chibi-Robo! (sort of), Shadow Man (sort of)


Open World Platform Adventures/Metroidvanias: 
Different to Metroid-likes in that progression is gated mainly by things like difficulty, quest completion, money and/or reputation, and in that they tend to feature larger worlds. World structure varies. I'm including games that have enough of an ability gating and exploration focus to appeal to Platform Adventure fans. 
Other examples: Outcast, Spider-Man 2, Gothic?, Incredible Hulk: Ultimate Destruction​
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WIP Souls-likes or Hollow Knight-likes:
PA/MV games with more elements from the (Dark) Souls series: heavily interconnected and non-linear world (at least in HK's case), corpse runs (probably influenced by Diablo and/or World of Warcraft), a checkpoint system to replenish health and respawn enemies (benches in HK respawn the tougher enemies), player vulnerability/immobility while healing, high difficulty and storytelling via pieces of lore found in the environment (originally from System Shock and RPGs). These games may also include online cooperative play or PvP, a stamina bar, character creation and experience point leveling though HK does not. 
Other examples: Gleamlight, Crowsworn, Ender Lilies?, Aeterna Noctis?, Playbound?, Blasphemous?
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WIP Roguevanias or Dead Cells-likes:
A combination of procedurally-generated roguelike games and PA/MV games. Since the game world changes every time you die, these are controversial among MV purists in that you don't get to familiarize yourself with a single world during your playthrough. 
Other examples: Rogue Legacy 1-2?, Eagle Island?, A Robot Named Fight!?, Ghost 1.0?, Sundered?, Endless Memories?
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WIP Brawlervanias or Beat 'em up-like MVs/PAs
​Pretty self-explanatory - These games feature significant elements from the beat 'em up or hack 'n slash genre (see Double Dragon or Ninja Warriors for example), within a MV/PA framework. I haven't yet decided exactly where this offshoot begins historically, but perhaps Secret Scout in the Temple of Demise (1991) can be considered the first since it often forces combat by locking you into the room you're in to progress. Or Spider-Man: Web of Shadows (NDS, 2008) since it combines this with more involved, combo-based combat featuring juggling and throws. 

Other examples: Princess Crown (non-platformer), Okami ​(Zelda-like), Darksiders II (Zelda-ish), Guacamelee 1-2, Valdis Story, Shattered Blade?, ​EXSYS?, Imp of the Sun?, ​Ori and the Will of the Wisps?, Darksiders III?, Salt and Sanctuary


WIP Outlier Categories (Pitfall II/Impossible Mission-likes or Hexen-likes; SMB3-likes; Kirbyvanias)
Here's a section for precursors and contemporary outliers to Platform Adventure games or Metroid-likes. The first category is for Maze Platformers with one big interconnected world or close to it and some form of gating and world persistency. Some of these start you off with tools or abilities needed to progress or let you find temporary ones, or if they're permanent they only have one use which is either for combat or functioning like a key. 

​Other examples: Aztec, Mountain King, Underwurlde, Bruce Lee?, Starquake, Cauldron 1-2, Fist II, ​Saboteur 1-2, Woody Poco/Woody Poko?, Takeshi's Challenge?, Rambo (NES)?, Impossible Mission II, Shadow of the Beast, ​Todd's Adventures in Slime World (small worlds), Clystron, Elf (AMI)?, Metal Mutant (PC/AMI)?, Dr. Franken (GB), The Addams Family (SNES/MD/AMI), Alien 3 (SNES), ​SOS/Septentrion, Umihara Kawase, Blackthorne, Montezuma's Return (GB/GBC, 1998), Spider-Man (GBC), ​Seiklus?, Mega Man Zero, VVVVVV (interconnected and non-linear but w/o ability gating), Blasphemous (no movement ability gating)
Non-side view: Ys V (SNES & PS2), Hexen: Beyond Heretic, Strife, ​​Realms of the Haunting?, ​​​Turok: Dinosaur Hunter, Hexen II?, Unreal?, Spyro the Dragon, System Shock 2 (sort of), Hype: The Time Quest​?, Mega Man Legends 2 (very minor ability gating), Spyro: Year of the Dragon/Spyro 3 (besides one level), Nox?, Baldur's Gate: Dark Alliance​, GTA 3 (open world)?, Ico?, Technomage: Return of Eternity?,​ Sword of Mana?, Ys VI: The Ark of Napishtim (overworld & dungeons)​, Gurumin: A Monstrous Adventure?, Mercenaries: Playround of Destruction (open world; besides some vehicle and bomb gating), Muramasa: The Demon Blade (Wii)?, ​Shadow of the Colossus?, Demon's Souls?

Another category was mainly popularized by some Mario games; in these games there's a separate hub map or area (using a different perspective generally) connecting the levels, you can sometimes take optional alternate routes (sometimes gated by temporary abilities), you use temporary abilities to progress or reach optional items that are given to you in the same level (note that the 2D Marios can be beaten using only the small form), and there are some maze levels (fortresses and ghost houses in SMB3-4). 
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Other examples: Commander Keen 2-3, James Pond 2-3, Star Wars (NES), Exile 1-2 (JP, ARPGs), Kid Chameleon (no hub map/area), Xargon, Spider-Man (MCD), Generations Lost, Kishin Douji Zenki (GG), Hyper Iria (mission selection menu), Spyro 1 (and most of 3), Jak and Daxter
Non-side view: MediEvil​ (very minor ability gating), Tomb Raider 3-4, 
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Lastly, even closer to proper Platform Adventure games are some of the Kirby games (Amazing Mirror and the Great Cave Offensive mode in Kirby Super Star) which have mandatory ability gating and an interconnected world, but temporary abilities which are lost either upon taking a hit or dying, and sometimes lacking world persistency. 

Other examples: The Castle and Castlequest/Castle Excellent (sort of),