Make the outside of the indoor "playhouse/room" to look like a real house. I would only of dreamt to have something like this as a kid. My kiddo and future kiddos deserve a kickass room they would be proud of.
Awesome Loft Beds--Since you won't have a window on the one end of your upstairs, this could be a fun idea for the kids area. Not necessarily a bed, but a 'loft' on top of a 'hide-out' area---or something. The bookshelf stairs are a neat idea too.
41 Clever Organizational Ideas For Your Child's Playroom