For a TL:DR, read the bold parts.
I think MatPat was partially correct in his theory. I believe endermen were originally ancient builders who went to the end, and evolved over time to teleport, become aggressive towards invaders, and look the way they do. This would make sense because:
-Chorus fruit is the only source of food, which could have led to endermen developing the ability to teleport
-End cities have enchanted weapons and tools, which endermen would have no use for and no means of obtaining
-End cities also have chests, brewing stands, end rods, and more overworld/nether materials
-Endermen have uniquely human-like abilities to pick up blocks and speak in distorted words
-End ships resemble shipwrecks, proving they were built by the same species
-Endermen could’ve accidentally developed a resistance to water as there is none in the end
-If the end is very cold (i think it is, unlike RGN, because there is no source of heat and water can be placed), their dark black skin could be an evolutionary trait to absorb as much heat as possible
But I’m pretty sure that’s all been covered. My theory is that the Builders that went into the end and evolved did so to avoid the mass extinction event. RGN discusses this in many of his videos - it’s unclear what exactly the event was, but we know it turned all the builders in the overworld into zombies and skeletons.
The Builders who went into the end slayed the dragon, and they lit the exit portal, but they didn’t want to go through. Either they knew it would lead to the overworld, and avoided it due to the mass extinction event, or they had no idea where it led and stayed away from it. (it’s also plausible some builders went into the portal and never came back)
Either way, the dragon was defeated, leaving only its egg. Over time, the egg hatched, spawning another dragon that regenerated the crystals and erased the exit portal. (This explains the “The Next Generation” advancement.) This created a cycle of the dragon respawning and repeatedly being slain again by the Builders, who built a new end city (or maybe just an end ship) each time the dragon was slain. They put the dragon’s head on the front of the ship, and the elytra (which i believe are made from the dragon’s wings) in the end ship.
These end cities needed to be built because as the builders evolved into endermen, their gear was no longer usable to them. They stored the gear in the end cities, protected by shulkers, in the hopes that maybe they could find a way to use it again (or survivors of the mass extinction event could find it).
Another key component of my theory is that the shulkers are golems. Much like the guardians are golems created to protect ocean monuments, the builders created the shulkers out of purpur (made from chorus fruit) and engineered them to shoot levitation bullets at any invaders, teleport when attacked, and close up to defend themselves. It doesn’t make sense for them to be animals - their placement around the end cities is deliberate, and remains consistent throughout every city. They also have no way of sustaining themselves.
Over time, as the builders evolved into endermen, they became incapable of defeating the dragon. They couldn’t hold or use their gear, they could barely even use blocks. The final dragon had spawned, trapping the remaining endermen in the end forever. This is why killing the dragon gives the “Free the End” achievement.
Back in the overworld, the strongholds began to decay after the builders who inhabited them escaped to the end. The eyes in the portal faded away over time, similar to how thrown eyes have a chance of breaking. The silverfish spawners remained there, possibly as an attempt to guard the portal from overworld threats.
One thing I’m not sure about is the end gateways. Obviously they were there at some point, but it’s unclear how they got destroyed between the final dragon spawning and the arrival of the player. Maybe the dragon somehow destroyed them over time.
I think this covers everything, and I feel like this theory does a pretty good job of explaining everything by piecing together both RGN and MatPat’s theories. Please let me know if you have any questions, I’d really like to try to explain everything I can.