Being able to explore the facility as a kid would justify all the rooms to me, so that feeling of "bloat" certainly would vanish. If past actions in the rooms could be seen as results in the future, it'd make these optional quests even more rewarding, even if just a visual change, or actually a locked door having a chest now.
Dragging the player into the world and almost immediately showing the domino effects of choices certainly would give the intro spice.
(And if you could tutorialize the skill to fight overleveled enemies through something like fighting against an adult as a child, I'm sure that gimmick/design would enter the player's strategizing much easier. I'll admit, I didn't get that's what it was supposed to be and didn't use the skill right while I played.)
