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Here's where you can find the theories on Subnautica.

Warpers are People!
Exactly what it says on the tin, the unreleased "Warper" creatures are actually humans that have either been re-engineered for aquatic life or were stranded (someone had to make those abandoned bases right?) and mutated into a fully aquatic species. Support for this is as follows: they've got a very humanoid appearance overall (head, chest, 2 forelimbs, 2 'legs', and then the 'cloak' piece) and they appear to have a large brain (large head). We also know this is an advanced civilization and that the planet has many strange functions and impossible creatures. Alternately, they could simply be sentient creatures living on the planet, possibly something to trade or live with in the future.
  • They may be aggressive towards 'normal' humans on account of being either abandoned on the planet or mutated/engineered against their will. Maybe they shot down your ship?
    • Interesting new evidence. At least in experimental, a PDA labelled "Degasi Voice Log #7" exists, with the Degasi crew realizing they are infected with a bacteria that can alter the genetic structure of living beings, and that everything on 4546B is infected, but can cope with it.
    • This evidence is due to be retconned and the theory Jossed.
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  • Jossed, The Warpers are cyborgs Frankensteined together from species native to several different planets, the Precursors made the bases before leaving/dying, and the pathogen mentioned just kills.

Lab World?
Could this be a planet for genetic testing to create new species for terraforming other worlds? That is, could everything on the planet be artificial, created through genetic engineering of different creatures into one creature? Here's the reasons to believe so:
  1. Crash - A species that is both a plant and an animal, the animal part of which explodes as a defense mechanism. That wouldn't evolve naturally, it's far too complex, but it *could* be created through artificial means.
  2. Crabsquid - Common, it's literally called a Crab-Squid. And it has the appearance of a creature that would result from advanced engineering of life forms to hybridize them for other worlds.
  3. Reaper Leviathan - Whale + Eel + Crab, maybe? Whale for size, eel for appearance, crab for those giant talon/claw/pincer/mandible things attached to its face.
There are more creatures that look like either hybrids of existing creatures or artificially created life forms, and they're all compatible with a human. Why would a completely alien world have so many plants and animals that are livable with humans, even if they may be a threat? Could be that the planet was chosen as a possible colony candidate for that reason, or it could be that the Aurora and crew were sent there to test the native life forms and see how well humans can survive on such a planet. Or perhaps sent to investigate why the planet was lost to humans (see above theory) and ended up being sabotaged.
  • Semi-confirmed. Planet 4546B is a lab planet, but it wasn't used by humans. The Precursors went there with a small team to research a cure for the Kharaa bacterium. They did find a temporary treatment, but before they could find the means to enhance it, the Sea Dragon Leviathan destroyed the Lost River base, releasing the Kharaa and effectively destroying the planet and reducing it to the state found in-game. Speaking of the Precursors, they either abandoned the planet or the crew deployed to it died with the outbreak. It eventually is left to the player's hands to finish what they started.

The Ghost Leviathan Egg
  • The egg in the lost river is either going to hatch into the ghost leviathan or is being protected by it. They have similar colors, are in the same area (if the ghost leviathan is going to be in The Lost River), and the egg is large enough to be a leviathan egg.
    • Confirmed: it is indeed a Ghost Leviathan egg.

The endgame is going to be to contact Earth.
The survivor will have to find a blueprint to make a transmission device to get off the planet and return to Earth. The game will end with them being rescued and sharing their experience with other people.
  • Either that or they will have to make the most of their time on the planet. They will have no way off the planet and die in underwater.
    • Semi-confirmed. Several Trello cards state the endgame goal is to construct a spaceship and escape.
  • Semi-confirmed there is a vehicle in development that's supposed to let the player leave
    • Confirmed. You do contact Earth, but after building said vehicle, leaving the planet for the nearest phasegate and return to Earth. then told you're not allowed to land as a punchline to a brick joke from early game

4546B is actually Earth, millions of years into the future.
After humanity relocated, and resettled on another system, they eventually died out there and reappeared years later. Millions of years after fleeing Earth, the abscence of humans has allowed new fauna and flora to flourish. 4546B's moon looks a lot like Earth's, and the red planet visible at night looks an awful lot like Mars; the next planet in our solar system. The backstory given at the start mentions the 22nd century; their 22nd century after humanity has resurged on another system.
  • Jossed. 4546B is located in the Ariadne Arm, while our system is in the Orion Arm.

A future update will feature another Aurora survivor.
This survivor will be a woman who also escaped, and will become either a helper and eventual love interest for the player character with whom they will reproduce to populate the world, or a character for use in online co-op.
  • With the announcement that female player characters are coming, this is ripe for a Static Role, Exchangeable Character situation: play as male or female, and the other becomes your fellow survivor. Or, if the devs want to account for a Gay Option, create two characters who then become Mutually Exclusive Party Members: something happens and you can only save one of them. An Adam and Eve Plot would only work if we assume our player characters have been genetically purified or something; mundane human genetics do not do nice things when your only mate choices are full-siblings.

The Reaper Leviathan isn't just a predator, but also a guardian.
The Reaper isn't just some highly-aggressive animal, but also part of the planet's natural defenses against external forces that the planet perceives as a danger. The planet sees humanity as the ultimate evil, seeking to exploit its resources for their own gain, so it somehow managed to destroy the Aurora and then sent the Reapers after the survivors.
  • Played with. The Reaper seems to be guarding one of the Lava Zone entrances.
  • Jossed The Precursors shot down the ship and the reapers have almost no brain anyways

other Survivors will appear in future updates.
As seen from watching Markiplier's videos, there are models of other divers in the game. A model of a diver can be found in one of the deepest areas of the game, but it has no motion and just stands there. Given the bits of start that says the other survivors were "collected" and the fact that the Aurora wasn't the first ship to crash on the planet, it's possible that there are some isolated pockets of humanity on the planet whether they are free or captive.
  • Those are size references used by the developers.

The Aurora was build to be both a spaceship and a boat.
If you know you're going to a planet that's mostly cover in water, it makes sense to build a ship that can make a water landing and float. The Aurora probably could have had it not crashed.
  • Jossed by what story exists. The Aurora was supposed to build a “phasegate” and was never meant to land.
    • But they had a secret mission to rescue the Degasi. It's likely they used an unnoticeable pod, but then again...

Fauna that exists in the concept art will always be canon, but the ones that you don't see in-game suffer a certain fate.
Based on Trello notes and Precursor data downloads, we can tell that the one Sea Dragon Leviathan in the game became the Unwitting Instigator of Doom (maybe not "unwitting," though) after it escaped and attacked the Lost River Precursor base. This caused The Plague known as the Kharaa to spread across the planet, killing 164 billion creatures in the process. The species that Bart Torgal noted as evolving to counter the Kharaa survived and thus are the ones you see in-game. But what about all the other creatures in the concept art? It's simple enough: they were simply wiped out by the Kharaa.
  • Alternately, they could just exist on far-away parts of the planet, possibly in similarly unimplemented biomes. Presumably there's lots of stuff on the planet that the protagonist never explores because it's too far from home base.

The planet used to have large land masses.
It's mentioned in some of the PDA's that an extinction event had happened in the planet's past, it's possible that whatever this event caused either the continents to sink or the oceans to rise. It would also explain why the islands have plants on them despite the fact that they typically don't last long (relatively speaking) as they are remnants of the former ecosystem. I also think some of the fauna are evolutionary descendants land dwelling creatures. (sea dragon leviathan, lava lizard, sea treader)

The Captain has an augmented immune system
Possibly everyone in the future does, it could be standard procedure for Aurora crewmembers. But that's why the Kharaa doesn't kill him like it did everything else on the planet, his immune system is more advanced.
  • Or he's survived the Kharaa for so long because he's been eating peepers all along...

if there is a third Subnautica, it will have the most dangerous non-leviathan enemy be called the Sharkcrab.
The original game had the crabsquid, Sub-zero had the squidshark, and this one will complete the cycle. It will have an EMP, just like it’s precursors.
  • Alternatively, it will be the Sharkeel, and the trend will continue indefinitely.

Handfeeding the Reapers
It is now possible to offer a Reaper a Peeper (and only a Peeper) and have it take the fish then leave you alone. Why would a predator that size care about such a small meal? It's made the connection between eating Peepers and not dying of Kharaa.
  • Possible, but also from a gameplay standpoint you can only reasonably handfeed Peepers. Video evidence exists of people feeding Ghost and Reaper Leviathans Peepers, Oculus (Oculusi?) which haven't been shown to have the enzyme and aren't really visually similar to Peepers (though that itself could be on account of the Reaper's eyesight and it might smell similar enough, genetic offshoot notwithstanding.
  • Also, the game engine is Unity, and under the hood, it could be all predators have a base script, and the taming mechanic got inherited code-wise onto the Reaper. Of course, you'd need to test if all predators can be fed prey fish.

The Cuddlefish is a precursor/Sea Emperor hybrid
What if the cuddlefish is a baby Precursor, or an experimental hybrid of Precursor DNA combined with Sea Emperor DNA? It shares the Sea Emperor's tentacles and has fin-like forelimbs not seen on many other tentacled creatures. Maybe the Precursors were trying to modify their own genome to naturally be immune as an alternative to curing Kharaa outright?

Cuddlefish were once domesticated as pets by the Sea Emperor Leviathans.
The PDA deduces that Sea Emperor Leviathan adults had to live in small groups to avoid exhausting their food supply, and their offspring spend only moments with their parent before parting company for shallower waters. Adopting pets would provide a comfort to Sea Emperors whose offspring have departed, as well as the potential for companionship without significant food competition. The swiftness with which cuddlefish bond with other species, despite living in a world so rife with predators, suggests their kind were accustomed to coexisting with, and being protected by, something much more formidable than themselves. The two species even share a similar body plan, suggesting that cuddlefishes' tiny tentacles may be aesthetically appealing to Sea Emperors, and could evoke parental feelings in them, much like how many toy dog breeds' large forward-facing eyes (similar to a human infant's) encourage humans to pamper them. You don't find any cuddlefish living wild, because they were too domesticated to cope once their Sea Emperor protectors were gone. Good news is that for every cuddlefish egg you can hatch, there's a young Sea Emperor Leviathan you can as well, so hopefully they'll find each other and pair up after you leave.

Refusing the player character to land is the last straw for Alterra.
The government which supersedes Alterra seems to be rather concerned with the safety of its citizens, given that it requires all spacecraft who receive a distress call to aid whoever sent it, regardless of the origin, and thus likely also has other individual safety-focused laws. Alterra seems to regularly abuse these; they are apparently infamous for using distress calls to get other ships to restock unnecessary supplies. Perhaps refusing a survivor of a spaceship crash to land until they’ve paid off a ludicrously large debt which they had to accrue to be able to survive is the last straw for Alterra, and they’ll soon be facing sanctions from the larger government and other governments within it for continually disregarding the needs of its subjects.

Subnautica and Hardspace: Shipbreaker are set in the same universe and Riley is the protagonist of both games.
Riley, the main character of Subnautica, ends the game being indebted to the Alterra corporation for a whopping 1 Trillion credits. Being that Riley is an systems engineer who was going to be working on a phase gate he is already experienced in industrial engineering in vacuum. Being that he despises Alterra and wishes to pay down his debt by any means, he decides to enter arbitration of his debt with Alterra and manages, after some negotiation and selling off his accrued materials to pay down some of it in the meantime, to get Alterra to knock his debt down somewhat for the valuable discovery of 4546b and the Kharaa Bacterium. Finally he reaches an agreement to have Alterra sell his debts off to another company. And where does his expertise in systems engineering in vacuum land him? An industrial company based on Earth named LYNX that happens to be looking for a skilled engineer for its Cutter program. Alterra sells his debt for a Billion credits, Riley applies for the Cutter position, and so Hardspace Shipbreaker begins.

The Fades from Natural Selection 2 are Kharaa-infested Warpers'
The Kharaa bacterium seen in NS2 is much more aggressive and much more deadly than the strain found in Subnautica, but the Warpers are suspiciously similar in build and behavior to the Fades. Not only do they both teleport around, they both have two arms ending in vicious bone-like scythes; at some point in the distant past, while the aliens were battling the Kharaa outbreak, the Bacterium successfully co-opted the Warpers and turned them into Fades.
  • Alternately, as the Warpers were evidently cobbled together from multiple different planets' species, the Architects and Kharaa may have simply appropriated those limbs from the same as-yet-unseen or long-extinct creature.

The abyssal-plain region was removed from the game for a secret reason.
It's because the game designers are setting up for a major reveal about the setting in a future sequel, that will take the sequential-gigantism patterns in 4546b ecosystems to their logical conclusion: that there is no land on the planet at all, and no "shallows" either. Rather, the entire setting experienced to date in the games has taken place on the backs of a few truly astronomical Reefbacks, drifting veeeeery slooooowly through the unbroken, thousand-kilometer-deep world ocean. The "lava" encountered beneath the apparent "seabed" is a part of these animals' thermoregulatory mechanism, the "caves" are natural pores in their sculpted mineral-encrusted backs, and the "hydrothermal vents" are excretory glands for metabolic byproducts. The various mineral deposits are cyst-like secretions from the mega-Reefbacks' skin, which explains why they keep re-growing, and all the organisms encountered are benign symbiotic endoparasites.

The Lost Pilot found the remains of the Mercury II's quarantined castaways.
Marguerit claims to have had nothing to work with but a repair tool and a knife when she washed up in Sector Zero. Yet, by the time Alterra begins its operation there, she's had a functioning home base, greenhouse, Prawn suit, and numerous pieces of equipment at her disposal for years. As she wouldn't have been equipped to dive down to the Mercury wreckage when she debarked from the Reaper carcass, it's likely that she found the cave where the Sol vessel's captain had reluctantly opted to abandon her Kharaa-infected crew members, rather than risk bringing the infection back to human space. Although those castaways were already decades dead by the time she arrived, their equipment - including, most crucially, a fabricator - gave Marguerit the "starter" gear she needed to survive at more than a cavewoman level.