Spy Kids/WMG

The series is set Twenty Minutes Into the Future.
Aside from the advances in technology, the culture seems to have become more Hispanic. Note that street signs and billboards from the first film are written in both Spanish and English, implying a bilingual society. Many experts believe the Mexican population of the United States will greatly increase in the near future; Spy Kids is obviously set after that has already happened. Add to this the vaguely-described "dark and confusing times" about ten years before the first film, which doesn't seem to reflect the early 1990s.
 * Always thought that was a Take That to the Darker and Edgier 1990's comics.
 * But doesn't it take place in Mexico?
 * If it did, why would the President of the United States show up so much? Not unless NAFTA has suddenly gotten much more powerful.
 * Maybe it's set in a post-secession Republic of Texas where the Anglo rednecks who spearheaded the campaign to secede got swamped by the Hispanic demographic wave, as Keith Olbermann predicted.
 * It appears to take place in Austin, Texas.
 * Or, it takes place in Mexico after being annexed by the U.S.

The Guy was a Guest Star Party Member built into the Game.
It was all but explicitly stated. The problem is that everybody (characters and audience) assumes that he's a player character and the game's creators were contracting Nostradamus. It's canon that  was both an AI and the Deceiver, so why is it so far-fetched that The Guy was a programmed character?
 * And he was a special unlockable that is only found if specific conditions are met but they never met him because of how they were playing, they never met him (they did have a cheat map afterall). He died so quickly because he was meant to show how difficult the final level is if you didn't find him before. If they HAD met him prior, he'd have been a Game Breaker to make the rest of the game extremely easy up to that point, including the final level. Note they said The Guy would've helpped win the unwinnable level IF you find him, they never did so he died, had they found him before, he'd have helpped them win the level.

The Guy was The Kid.
He gets killed with one lighting attack, right?
 * Also note that he got killed in a Guide Dang It trap that was impossible to see coming.

In Response to the Above
We all know that the full title of I Wanna Be the Guy is I Wanna Be The Guy: The Movie: The Game(and if you didn't know, now you do). We were all meant to believe that was a joke, but little did we know Spy Kids 3D is the fake title for I Wanna Be The Guy: The Movie, which everyone's favorite game form of masochism was then based off of.
 * Or: It's really I Wanna Be The Guy: The Movie: The Game: The Movie making the video game adaptation I Wanna Be The Guy: The Movie: The Game: The Movie: The Game, as was prophesized by the ancient ones (read: some troper) who wrote the IWBTG page (it's the Colon Cancer example).

Juni and Carmen are now trapped in a virtual reality world.
This is how the virtual reality creations supposedly got into the real world and why the last few scenes of the third film made no sense whatsoever. It was cobbled together by the Big Bad to make them think they'd defeated him.
 * That's disturbing, and yet it makes so much sense.

Disney forced a Gecko Ending
They found themselves with a movie that could only have a happy ending if they sacrificed logic. It's a children's movie, so they didn't want an unhappy ending. (Hey, even Old Yeller has what's intended to be an upbeat postscript.) Thus, the ending that's there.

The Guy was killed because he failed a Quick Time Event
A really annoying Quick Time Event that requires spilt second timing, with an invisible prompt.
 * Maybe it's a Dynamic Difficulty event, which requires you to react once for each life you have left within a certain amount of time. If you have five lives, it's quite difficult. if you have one or two lives, it's pretty simple. If you cheated extra lives into the game, or you're an NPC and the dev team forgot to make an exception for you, it's effectively impossible.

Carmen will grow up to have a daughter...
...named Marni. The rest is history. Uncanny family resemblance abounds, to be one day remarked upon by said (now-late) daughter's best friend.

Spy Kids (the first one at least) was made by Buster Bluth.
The movie is extremely childish, involves two kids on their own away from their parents (reflecting Buster's own secret desire to be rid of Lucille), and of course, there's a strange obsession with hands.

The women in Ingrid's family are genetically predisposed to be attracted to Latin Lovers.
This is pretty much canon. I mean, one of them married Ricardo Montalbán and then her daughter married Antonio Banderas. Could also be a case of Like Parent, Like Spouse.

The Machines have won, and everybody is trapped in the VR for the rest of their lives
The only way to stop the machines was the transmooker device, which was destoyed in Spy Kids 2 - it was all a Xanatos Gambit to stop the competition. The Toymaker is really the architect. Not sure who is The One, its one of the main characters.