The sudden appearance of the mutant Descendants seems strange at first. Especially, after fighting a few and finding no place to hide. Until it finally hits you: they make taking cover useless. Meaning that the mechanic that you have been accustomed to for the whole game is no more. Rather than being an Unexpected Genre Change, it DOES make them much more menacing. This is much more apparent when you have to battle both the mutants and the mercenary soldiers at once, forcing you to alternate between tactics.
Nathan's dialect when speaking Indonesian is probably what gives him away, since it's noticeably different from what the inhabitants of the area would speak.
The Early-Installment Weirdness of Elena being the reckless person looking for more adventure while Nate wants out makes sense: even if his ties with Sully aren't what they'll become, he still just seemingly lost a good friend right at the start of the adventure and wasn't out to pick a fight with Roman's entire criminal group. Pirates, he can handle - an entire army of military-grade mercenaries out for blood, not so much this early in the series. Elena on the other hand just got screwed out of a boat that wasn't insured because of Nate, is desperate to get footage of whatever she can come hell or high water so she's not effectively stuck in debt, and Nate just happens to be her only ticket to making that money back and then some. By the time everything's wrapped up and they've survived the seemingly-impossible, Nathan ends up with a thirst for more great adventures even if he's more cautious, while Elena had her fair share, nearly bit off more than she could chew several times over and ultimately becomes the voice of reason by comparison.
Why the enemies don't use handheld machine guns? Because is impractical in the game's environment where a certain agility is required and because the antagonists of this game have less resources compared to the antagonists of the following games.
The ending only had Nate defeat the villain. The mutants on that island still pose a threat to people that might want to explore that area in the future. Hopefully no one will ever think to venture there, and if so the mutants will have died out with El Dorado buried in the depths of the sea.
The mutants were created by the virus inside El Dorado. The REAL question is, where did it come from?. Or more pressingly, exactly what is the corpse inside the statue? It's not just another mutant, it looks nothing like them.
In the ending cutscene of the first chapter, Nathan mentions casually that Francis Drake and his crew assaulted a Spanish float, stealing the documents that we see in Drake's journal in the game. But why did that Spanish float have the documents of the Island? It's because those were the ONLY survivors of the attack of the descendants, meaning that Francis Drake and his crew killed people who were deeply traumatized and shocked about what they had just survived. Nate, your ancestor wasn't so nice...
