While there are certainly a large number of Pokemon one would consider "useful," Ditto in particular is highly prized for its ability to copy other Pokemon and their abilities, as well as its status as one of the best breeding Pokemon. However, its Transform ability is a double-edged sword.
Not only can the little pink blob transform into Pokemon and inanimate objects, but it can change into humans as well. Considering the large amount of evil factions within the Pokemon universe, this is actually rather terrifying.
Initially, Ditto was valued for its ability to breed with any Pokemon it's left at the Daycare Center with. Usually, the two Pokemon must be of opposite genders and must have at least one of the same Egg Group, or type (ie. Poison, Metal, etc). You can't leave a Flareon and a Golem and expect an egg to be waiting when you come back. However, Ditto has become a staple in Pokemon breeding because it's gender neutral and can adapt its type to match that of its partners. It's also the only Pokemon that can breed with other gender neutral Pokemon. So it's one of the most useful Pokemon to have in your stash as a trainer.
What isn't really talked about is how that ability can be used for more nefarious actions. The idea of a Ditto taking on the form of a human has been talked about among fans for years and seemed to be solidified as a possibility in Pokemon Ultra Sun and Ultra Moon, when a group of Ditto begin impersonating humans. However, these Ditto can only say their own name, so it's not a perfect transformation. Pokemon:Detective Pikachu also explored this idea when it revealed that Ms. Norman, the assistant for Howard Clifford, was a genetically enhanced Ditto. This Ditto was forced to wear sunglasses though because it wasn't a complete transformation and still had the dotted eyes of its natural form.
Originally in the anime, it was only one specific Ditto that kept its beady eyes, though that canon seems to have changed to include all Dittos seen later in the series. Clifford's Super Ditto was also able to transform into other Pokemon without having to face that Pokemon at that moment. It changes from a Loudred to Lucy to a Machamp to a Cubone quickly and without a problem, minus the eye thing.
An ability that has been valued for its place in Pokemon breeding suddenly becomes more terrifying when thinking about how it can be used to harm others. Imagine the horror of finding out someone who had a grudge against you had their Ditto turn into a copy of you and framed you for a crime. Unless you had a viable alibi, and we assume that Ditto can also copy things like fingerprints or DNA, you'd have no hope of being found innocent in a trial.
There's also the possibility of someone completely stealing your identity using a Ditto that can perform a complete transformation. Not only that, but someone could use a Ditto to turn into a gun and use it to kill, and the weapon would never be identified -- the striations left on the bullet would match a gun that no longer exists once the Ditto changes back.
So despite how much trainers love this cute little gooey pile of pink, it's actually got the capability to be more dangerous than anyone realized. While the average trainer wouldn't think to use their Pokemon partner in such a way, other shadier characters wouldn't have any trouble coming up with ways to take advantage of Ditto's powers.