Where on Earth Is Carmen Sandiego?/WMG

The Chief placing his memories in storage every fifty years was a voluntary decision.

 * Think about it, if we have hard drives ranging in terabytes now, storage space on a system a hundred years from now wouldn't be much of an issue. Then we have his reaction to Carmen's faked death... given that, his reaction to her really dying, and to Zack and Ivy passing on would probably be as bad if not worse. Who Wants to Live Forever? would be kicking in around then, but since he likely couldn't self-terminate, sacrificing his memories is the next best thing.

The future Chief met in 2101 actually ISN'T the same AI as the one in the present.

 * Between hardware differences and upgrades, there's a chance that while on the outside he looks similar, within he's probably a very different being. The memory archives are what's left behind when Acme switches to a new AI.

The Chief and the Acme mainframe are a set of magical Devices.

 * The mainframe is a massive Storage Device like the Tome Of The Night Sky, dedicated to storing information rather than spells. The Chief is it's control program, possibly a Unison Device like Reinforce, but he'd be more of a support mage like Yuuno (shields, bindings, illusions and teleports) rather than an outright Person of Mass Destruction.

Armando Arguella is secretly a VILE henchman.

 * It's strange that of all the Guest Star Acme Detectives Zack and Ivy have worked with, Armando is the only one who has a last name. Think about it - with the exception of Suhara (since that's his last name and his first name is never given) and possibly Lee/Li the Macau detective, none of the current Acme detectives (including Guest Star Acme Detectives) have last names. The detectives that do have last names have since defected and become thieves (Lee Jordan, Carmen herself). And in the cases where Armando's worked with Zack and Ivy, he somehow manages to turn circumstances of the case from working in Zack and Ivy's favor.

The Players are actually in-universe rather than outside the fourth wall.

 * They're potential Acme recruits that are too young to officially join, but are getting trained by being allowed to shadow actual detectives via that computer program they all use.
 * That might explain what happen to the Player's computer at the end of Deja Vu.

The entire show takes place within the Player's imagination.

 * He's playing one of the old DOS versions of Carmen Sandiego and daydreaming about what could be happening in-game, while adding his own unique twists and plot points.

Acme keeps a lot of VILE's transport crafts for training purposes.

 * Given that more likely than not VILE's crafts are probably customized for Carmen's purposes (justifying every VILE employee's Universal Driver's License), it might explain why Zack can operate a fair number of VILE vehicles and hovercrafts but not the C-5 car.

Carmen Sandiego is actually Dora the Explorer as an adult.

 * She's a vaguely Hispanic character, obsessed with maps and education, teaching kids about geography.
 * Don't forget the ample Multilingual Bonuses in both cases.
 * Not quite multilingual bonus, really. I don't recall any cases of the Spanish (or other languages, as the case may be) actually meaning anything other than what was described in subtitles.
 * But Dora the Explorer has parents; Carmen was an orphan.
 * Dora's parents were archaeologists; it's pretty easy to envision the various ways death could have befallen them.
 * Except, isn't it hinted that Carmen's father might still be alive, or at least that she isn't sure who he is?
 * Wouldn't this make Dora's cousin Diego Sandiego?
 * She just got tired of fighting crime, and went over to the dark side.