Honestly I am a bigger fan of the changes done to the story of the first game, both by how unexpected they were and how such changes expanded the bigger story.
In general, the way the story of the second game was told in the manga felt way safer, even with the changes, which didn't add much and I think some things were lost in the transition, giving so little time to Hanna and Jihl's roles in the story made it fell weaker to the game's in my opinion, maybe it has something to do with the limitations of adapting a story that's not over yet, while still having to keep up with the releases.
Speaking of which, I am extremely excited for the third game, easily my most anticipated game of the year. Thank you for translating the manga, I'm also looking forward to how the manga will adapt the final chapter of Fuga.