[[WMG: The chips being EMP-sensitive was not the real main reason the military didn't adopt the X1000]]
The real main reason was that someone in the military [[GenreSavvy realized that]] [[AIIsACrapshoot giving military equipment intelligence and the ability to learn isn't all that good an idea]]. The reason they didn't tell the designer that is that they didn't want to [[WrongGenreSavvy offend the genius capable to making chips with those capabilities by rightly implying he was a moron for not realizing that himself]]. It not being all that cost-effective to give something that will be used for significantly less than a day (any single missile) the ability to learn might have contributed, as well.
* Of course, given the way that the toys reacted to having the chip installed, that is the shift to the extremeness of what was originally reasonable personalities ('Defend Humanity at all costs!' and 'Learn about this strange new world!'), we could assume that any missile with the basic instructions of 'Be fired, fly through air, destroy the target' would become a zealous engine of destruction for it's singular purpose. Whether that is a good thing, however, is still up for debate...
* The original plan may have been for it to be installed in a remote guidance system that could learn from several launches.
[[WMG: There will eventually be a sequel some time in the near future.]]
[[WMG: The X-1000 will later be used to create [[TheTerminator Skynet]].]]
The Commando Elite? They're the first Terminators. Scale them up and replace the Gorgonites with humans, and you've got genuine Terminators. Almost every trait of Skynet and the Terminators is shared with the Commando Elite: They relentlessly pursue and destroy their targets, they're single-minded and impossible to reason with, they're capable of learning, they ruthlessly exterminate anything that comes between them and their target, they have a human-like appearance despite being machines, and they keep coming back until they're completely pulverized. (Just look at the scene where Major Chip Hazard is disfigured, but comes back and tries again.) Terminators are also shown to have a chip inside their heads that's so important that they shut down if it's removed--it could easily be a later model of the X-1000. Finally, the movie ends with Gil Mars looking into using the X-1000 for military purposes against the USA's enemies...just the way that Skynet started out.
The only inconsistency is the X-1000's weakness to EMP, which the Terminators don't seem to share. However, the creator of the X-1000 mentioned that practical shielding for EMP exists, but wasn't cost-effective. Clearly, Skynet wasn't so concerned with money, and made sure to equip all of their Terminators with the proper shielding to counteract this weakness. They probably learned from the failure of the Commando Elite.
[[WMG: This movie takes place in the Toy Story universe.]]
How else would they be able to bring a bunch of Barbies to life. Unlike the commandos and Gorgons, they have no chips, no motors, no sensors. One salvaged chip and a machine out of Frankenstein wouldn't be enough to do that. Solution, the toys are already alive, the chip just corrupts them. Essentially it turns them into violent Buzz Lightyears.