Numbering your points will make things easier to respond to next time.
Tattoos are only story based for now. Later I will add a shop.
Pregnancy is meant to have pros and cons, but not feel like a punishment. So yes, places where content is lost will be reconsidered.
Sweet girls pregnancy thing is because it's incomplete. Will be updated soon to properly reflect things like this.
Haven is the last institute mission currently
Cass/Mira will play a role in a currently under development quest. I have laid the groundwork but not completed it yet.
Broken events in the school are temp for now.
Like above, the Cass/Mira stuff is still under development.
Pub will keep getting content additions as development progresses. I want fewer, content rich jobs as opposed to many shallow jobs.