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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ass Pull: So a man on the street that they were gambling against just so happened to have a map leading to El Dorado as the Spanish fleet were going to South America AND just so happened to land right where El Dorado was?
That man was a member of the crew looking for El Dorado, they likey all had a copy of the map which is why you see them following the same trail that our heroes took.
Others have also jokingly compared to Thor and Loki. Which means they are gods. Especially funny since Miguel directed the first movie.
Ho Yay: Dear God! The relationship between Tuilio and Miguel drips with this. From their naked bathing together and Miguel's jealousy at Tulio and Chel. Indeed, the film works best if you go through it under the assumption that the two are repressed (or even not so repressed) homosexuals.
They were originally going to be lovers. A trace of this can still be seen in the original subtitles, which have them refer to each other in romantic endearments, though whereas they were reintended to be sarcastic is unknown.
There are quite a few scenes where you see them acting rather...intimately with each other for just a second. And the endearing looks that pop up more often than not are a dead give-away, too.
To be more specific: It's obvious after the ball game, where Tulio and Chel are standing very close to each other, being pretty touchy feely. Not a second later (after the "camera angle" changes) Tulio has his hand on Miguel's chest and Chel is standing about three feet away. The animators apparently really wanted to keep the original relationship in the movie somehow.
Also, after they lose each other during "The Trail We Blaze", Tulio and Miguel put their hands where? Hips and shoulder, respectively. Very...coupley...
Gifs of Miguel's intense lute playing during the gambling scene are quite popular on Tumblr.
What Do You Mean, It's Not for Kids?: It's not an adult movie, but it's certainly no kiddy film either. Which badly hurt marketing and ticket sales, leading to disappointing revenue - the campaign was aimed for kids below ten and no-one else.