My First theory is that Of the creation of Spawners being down to an overworld Boss which Mojang havent Introduced, or previously Considered introducing but never did. Spawners can be Both negatives or Positives for Players. They can be negatives because some Spawners can end the life of a Player pretty swiftly. However if respected by the player, the player can use them as a Grinder. However, this theory Has a large amount of Problems with it When looking at Cavespider spawners Existing in Abandoned Mineshafts. As Logically a Boss Mob wouldnt need a mineshaft.

My Second theory is of a race seemingly Existing before the Player. It would have to have been a Long time Before the player though, as Often structures such as Strongholds and Abandoned Mineshafts are broken and in Disrepair. This Would easily account for the Deepness of Dungeons, and the Presence of Cavespiders in Abandoned Mineshafts. And the Creation of the Abandoned Mineshafts, and the Strongholds. Does this Theory Hold water when looking at the object "Spawners"? Perhaps it does, It is possible to Imagine the Prior Race placing Spawners and Other traps to harm the Player, such as Silverfish in Strongholds. However, if these Structures are so Old why is it Some of them are so close to the surface?

This Third and Final theory is Very similar to the Second, but with a Few Minor differences. For starters, the Structures arent as Old as they Appear, Abandoned Mineshafts were Built in order to Obtain goods for the Prior race, As there are Many in One world, it would suggest they were in a Hurry to gain as Much as they could. This would account for the Chests in the strongholds and Abandoned Mineshafts. The introduction of Dungeons could have been a trial for the warriors of these races. This Would account for the Dungeons without Chests. As the warrior would have to retrieve the chests without Death. Once warriors were Chosen they would Be sent to the End to join the Endermen and the Dragon, whom this Race worshipped.

However once again this theory has Flaws, such as the Cavespider spawners in the Abandoned Mineshafts, and the presence of 3 Strongholds with Portals in the world. This even Pushes the Question of why Nether fortresses Exist in the Nether.