1. The question of if MC can - or should, or wants to - free Chloe from his control or bury her old self permanently will be a big part of her storyline in Act Three :)
2. Yes, and you will also have the chance to recruit her as a "Battle Form" for Chloe for the Combat system later on too.
3. Chloe's Fey Forms won't be able to get pregnant, as she can't hold the form that long, and when she phases back into normal the Fey Form dissipates back into her energy signature.
4. I don't think that's a question..? ;P
5. No spoilers for the future story beats of characters, sorry!
6. If you didn't bring her with you in the finale then yes, you'll have the chance to find her again later. If you did bring her with you then she'll appear in the Manor once I get around to coding her events in.
7. No spoilers for upcoming bosses, sorry! I want some of them to be a surprise, and some of them to show up in the sequels.
8. Emmett (along with Erica) will reappear, but they're side characters so don't expect too much in the way of story impact.
9. Nobody really understands the Ard/Hana situation. In a world of magic, anything is possible, but MC doesn't have the time or resources to focus on researching how to split the two - and they're perfectly happy with their situation right now anyway :)
Hope that answers everything!