If you could do it over again knowing what you know now, what would you do different? Purely as a thought exercise; I'm just curious about your views on it all.
My first thought with everything that is happening today (the CC companies, Patreon, etc) would be to make Klara and Sky normal characters for story purposes, leave them as the MC's mother and sister, but save them for another project (weren't you working on something involving the deities from your universe?). Then bump Lily up to a main LI and give her some of the time that had be allotted to the other two. However this can only go so far as I have no idea what else you have planned. And yes I know this would piss off the incest crowd, and I am okay with that. An even simpler solution would be to move Lily to a new project and just use MBIML to build up her character a bit.
IF I could do the game all over again, from scratch, a lot would change, especially how I set things up during the premise. Everyone will no longer stay with you in the same house, only Klara and Sky
(I'd still keep the childhood friend and guardian thing because that's the most essential part of the main story).
Aine will come looking for you herself through Emma. She'll try to make peace with you, and we'll take things slow from there. Instead of entirely moving on from the past, she'll redeem herself through your character dynamics and such.
Emma and Gwen will come follow in the middle of it.
Introducing Moon and Freya to the story later on.
Chapter 1 - Episode 1 will be moved to Prologue.
After that, I'm satisfied with what happens further into the game.
Remove Lily and Naomi from the story. They were unnecessary characters added on impulse.