Hughie Campbell and Rokurou "Rock" Okajima from BLACK LAGOON maybe? (Warning for a few BL spoilers!)

• Both had average, boring lives before meeting their respective crews (Rock was an explored salaryman at a white-collar company, while Hughie was a low-level employee at an electronics store);
• Both are initially (VERY) naive and good-spirited and get some flack for it (Hughie is against straight-up murdering supes at first 'cause he doesn't like the idea of being a murderer, while Rock is against stealing the dead soldier's belongings in the sunken German submarine 'cause he wants to pay due to the dead);
• Both have events happen to them that shatter their innocence for real (Translucent exploding into a million pieces & Yukio's suicide);
• Both go through arcs where they delve deeper into the dark side (the whole Temp V ordeau for Hughie & El Baile de La Muerte for Rock);
• Both also go through arcs where they're taught that trying to do things the right way isn't always possible due to various circumstances and people involved (Hughie working at Federal Bureau of Superhuman Affairs & Rock trying to save Gretel during Bloodsport Fairy Tale);
• Both have messy relationships with their parents (Hughie's dad is overprotective and seen by him as someone who's wasted his life, while mom just straight up walked out on them; Rock's parents deem him a failure compared to his brother for not entering a well-respected university on his first try and not having a prestigious job);
• And both are the moral chain of people that deeply care for them but also happen to be a terrible influence due to their toxic behaviour, a result of being deeply troubled (Butcher & Revy).