The Road to El Dorado/WMG

Elton John was there the entire time
This would explain the music video and how no one really notices animated him. He was probably a crew member that sneaked into the rowboat behind Altivo :P

Miguel and Tulio are prophets of the gods.
To protect the people of El Dorado from Cortes, the gods used Miguel and Tulio to get rid of the treacherous high priest and shut the passage into El Dorado. That is why the armadillo can fly about during the ball game. That is why the volcano erupts and then stops on cue.

It would also explain how everyone seems to be speaking the same language.

Chel is also one of their prophets, though she doesn't know it. If she hadn't stolen the relics, then Miguel and Tulio wouldn't have found their way into the city. This gives us the Rule of Three, since the three of them being the prophets of the gods. As we all know, those gods sure do like things that come in threes.

The volcanic eruption happening just when two guys masquerading as gods need proof of their godhood? Too much of a coincidence NOT to be some form of divine intervention.

The Map was Magic
The Treasure Map was magic, which is why it was an accurate depiction of the new world despite nobody ever being there.

It may have been created by the Real Gods to lead Miguel and Tulio to save El Dorado.

Chel is a slave.
Notice that she was the only El Doradan native who wore white and no gold. The white could be a visible marker of her status as a slave, and why would anyone let a slave wear gold?

She's the only slave we see because the rest are out working. She's only there because she was considered the personal servant of the Gods. This would explain why she wanted that particular pair of earrings so much -- it would mark her status as a freed slave in combination with her white clothes -- and why she wouldn't tell the guys why she wanted to leave. She thought that they wouldn't let her join them if they knew.

Chel was a prostitute who sidelined as a thief.
This would explain her suggestive clothing.

Chel isn't an "El Doradan native"
She was originally from some other civilization. It was conquered and either enslaved or assimilated in a second-class way by El Dorado. It's also possible she's the Last of Her Kind.

She knew the way out of the city. She has the clear white/no-gold status markers mentioned. She feels no loyalty to the city AND doesn't believe in the religion that every (other?) citizen shown reveres unquestioningly.

She also refers to getting out as dreaming of "bigger things"...while living in a city made of solid gold.

Chel was a slave of the high priest and intended as an eventual sacrifice.
This would explain her being well-educated about religious matters despite her not believing in the religion. It explains why she suspects, and perhaps even already knew about, the sacrifice that surprised everyone else -- including the chief -- when the high priest wanted to give a "proper tribute". It also explains her feeling SUCH urgency to get out by any means necessary.
 * Word of God intended for that to be the case, but cut it out of the original because they didn't want to show the city too early (it was in the DVD commentary.)

Miguel knew Cortes and Altivo before the movie started
Sometime in Miguel's past, before he met Tulio, he learned that Cortes sucks and that Altivo is awesome. It would just ... explain so much. No, listen. Despite Cortes being a national hero or something, Tulio doesn't seem to know anything about him except that he's bad news. Miguel, on the other hand, looks like he definitely knows this guy. When they first see him at the ship, it's Miguel who says "Cortes!" with an expression of shock and horror. (This is the same guy who thinks that Cuba is a good thing). Miguel's supposed to be the carefree and optimistic one, but he's the only one who is concerned about Cortes and his evil plans.

He also seems to be familiar with Altivo. He COULD have learned Altivo's name by listening to people talking on deck, and his instantly loving the horse could be Miguel being a Friend to All Living Things. But Miguel literally jumping ship to save Altivo instead of helping Tulio makes more sense if he was already attached to Altivo.

Perhaps Miguel's family once owned or even bred Altivo, and Cortes eventually obtained him from them, legally or by force (or both).

Miguel is able to tell what Altivo was thinking at several points, such as "OH, he wants his apple" as if he should've realized sooner. Granted, Miguel IS a Friend to All Living Things, but Altivo specifically gets a good deal of recognition and attention.

"Miguel" is an alias
He's blond and he has blue eyes and a British accent. He's originally from Britain and hiding out in Spain.
 * He was an Englishman named Michael called "Miguel" for convenience. He was just a rover, not necessarily a fugitive.
 * We have to assume that they're speaking Spanish, which we're hearing as English thanks to Translation Convention. Thus, Tulio and Miguel aren't really using an American or an English accent, but the accents of a Spanish local and a fluent foreigner. Miguel may be Basque or Andorran, or, less likely, Portugese or French. That doesn't rule out the possibility of his real name being Mikel, Miquel, or Michel.
 * But there is such a thing as a blue-eyed, blond-haired Spaniard, you know.

Miguel is in love with Tulio.
This would explain his jealousy and hurt about the thing between Tulio and Chel. Yeah, they're best friends, and Tulio acted like an ass towards him because of Chel; but Miguel's reaction is still exaggerated.

There is also something stereotypically gay about him, what with his effeminacy and all. He would have to be bisexual, considering the thing he says about "the girl in Barcelona" and his own drooling over Chel when they first meet her.

The writers toyed with the idea of making their relationship a sort of "wink wink nudge nudge" thing that would be fairly open but would fly over the heads of children. If you watch the movie with subtitles, then you will see that they left in a few endearments. ""Dinner is served dear.""

More to the point: ""Now you have all your precious gold AND CHEL, so what do you need ME for?""

It's obvious just what role Chel was filling, what with that scene of them in the floor. This strongly implies that the guys were in a relationship.

Miguel and Tulio died in the storm.
El Dorado is their Dying Dream. Connections to our history put the movie on the Mind Screw end of the Sliding Scale of Fourth Wall Hardness.

Horrifying as that is to think, it would also explain both the lack of language barrier and the city calling itself 'El Dorado'- the same name outsiders who had never been there and were unsure of its existence of had for it.

That wasn't tobacco in those cigars..
Notice the party sequence gets gradually stranger as it goes on and they keep drinking more and more. Then they SMOKE. Suddenly, things go COMPLETELY over the edge in a matter of seconds.

The volcano was conscious.
And it obeyed Miguel and Tulio because IT thought they really were gods.

The ARMADILLO is the real god!
Watch it carefully; every time something crazy is happening, it's emphasized. In the creation myth intro, there are armadillos. When the volcano is going off, the armadillo is dancing about; it stops when he does. Then there's the magical flying of said armadillo during the ball game, of course. The list goes on. Mayhaps accidentally saving him while blazing their trail was luckier than our Spaniards thought?

OF COURSE!! It all makes sense! Planting himself where the snake would menace him was a Secret Test of Character, and by saving him, our heroes passed, and he watched over them in all their endeavours!
 * Albeit saving him accidentally.

Word of God says that this was one of the alternate endings, where he is revealed as god/angel sent to help Miguel and Tulio.