The early game needs a bit more (re)work.
- If you haven't kissed Eliza before the last night in Riverside, the conversation about her father is skipped. The next day, when they leave toward the capital, the MC will casually mention Eliza's father teaching him things, and she doesn't react to it, as if that conversation happened anyway.
- In Riverside, after the MC gets slapped, Eliza says he should run after Alice. If you pick the dark path, the talk with Alice gets skipped but doesn't influence any other conversations. He'll tell Flynn that he talked to Alice in the next scene, and Alice will know things that she hasn't been told when walking her home after the bar.
- If the MC never told Eliza about his past, she's not visually surprised when the bartender mentions it. The MC shuts him down but is all over it on the next day when other people discuss it. Personally, I think the choice about telling Eliza about the MC's past at the very start of the game would fit better right before they arrive in Riverside.