All the main villages are crooked in some way.
1. Mist is the worst. Genin graduation exam is a fight to the death. Plus the Kiri villages hates people with KKG. Both the Yuki (Haku) and Kaguya Clans (Kimimaro) were wiped out by their respective village Kage and Jonin.
2. Cloud has a history of stealing jutsus from other villages and kidnapping people who have special abilities from other villages. Both Kushina and Hinata were victims of Cloud plots to steal and study the special abilities of their respective clans. Even Ohnoki called Ay out on this practice during the Gokage Summit. Saying Ay couldn't be trusted. Ay and his father A were both warmongers who threatened to attack other villages over "imagined" slights. Plus, the attempt on Tobirama's life under a flag of truce when he visited the Cloud village.
3. Stone openly admits that it hired the Akatsuki to do jobs for them and we know what the Akatsuki members specialize in. Murder and assassination.
4. Sand's Kazekage killed his own wife to turn his son into a weapon for the village, and then tried to kill his own son several times. Plus, the Rasa allied himself with a known terrorist (Oro) and his Sound village to destroy the Leaf and kick off a world war. Despite the treaties and alliance the Sand had with the Leaf.
5. Konoha's dirty laundry stems from things Danzo did to preserve the Leaf and keep it's interests strong. The Uchiha Massacre being the most egregious, but at the same time, the Mist killed all the Kaguya's because they were also planning a coup. Remember, Hiruzen didn't agree with the Uchiha Massacre, but at the same time didn't have any qualms about it being done after the fact. Just like Oro's experiments on 60 babies to recreate Moukuton. Hiruzen had a chance to stop Oro, but did nothing when the time came. Danzo kept the notes and over saw Yamato's training. The same way Danzo employed Sai and Kabuto from youth, to adolescence. Danzo also joined covertly with Hanzo to quash the rising Akatsuki in the Ame village before they became the big threat of part 2. Danzo doesn't operate in a vaccuum though. People knew what he was doing but no one figured it was their place to say anything.
All the villages have problems. The Leaf is just the least offensive.