If you didn't want to to bunk beds, you could have twin beds on each side of the room with two bookshelves separating the room (one bolted to the wall and the other bolted to it to prevent tipping). That way it would create somewhat of a partition but not enough to take up the whole room.
On the backside of the bookshelves (since each child will be seeing their bookshelf, plus the back of their siblings' bookshelf) you could paint it with magnet paint, then paint it over the magnetic paint with chalkboard paint -- that way the backs of the bookshelves will have use -- both magnetic and chalkboard. in the bookshelf facing each child you could have baskets containing their toys, and of course, books.
A couple of floating shelves over each bed (make sure to put them high enough so the child won't bonk their head upon sitting up!) would provide more storage.
A small trunk in front of each bed could provide more storage and would provide seating.
If you can't paint, you can do removable wall decals like this
and to add more privacy (your daughter most likely will want/need this more since she is entering pre-adolescence), something like this
would be cool.
I like the hanging doodads
from ikea -- keep in mind they are not only great for toys, but can be hung in a closet and can hold socks, undies, even clothes since your kids are still pretty small.