The secret in MI1 is that Monkey Island harbours, indeed created, an undead LeChuck in its catacombs. This is hinted at in the very first cutscene of the game: “Meanwhile… Deep beneath Monkey Island, the ghost pirate LeChuck’s ship lies anchored in a river of lava.” LeChuck describes the place as “hell” implying that it’s a literal hell for the dead to be reborn as ghosts, and his first mate is revealed to be someone he murdered to create a ghost. The only reason you don’t “learn” this secret is because you never see the ghosts being created in MI1 (though as mentioned by @BaronGrackle you do see it in Curse), but that’s the secret I reckon.
The ending to MI2 is not “the” secret but rather a part of the puzzle as I see it. You can choose to go along with the idea that there are two rowdy boys playing silly buggers in a theme park and letting their imaginations get away from them, but it doesn’t change the secret of the original game which didn’t have a theme park. Plus the brothers scene from MI2 is a Star Wars parody anyway.