I still think going with the page per scene system is a good solution. It's not very complex, and it's not like all Ages will require to use several pages or PRPs.. (animations and GUIs not withstanding) The visibility problem is indeed an issue, but the more I think of it the more I realize it's not something that will be that troublesome. The linked objects solution works, and although you'll need to delete duplicated objects it's not that big an issue.. Plus again, I'm pretty sure more than half of the Ages will not need several pages; I'm looking at the Ages I have downloaded and that's certainly the case. And those who do use several pages don't really need to anyway.
That looks like an interesting solution. I understand why some people might all this needlesly complicated, but again most Ages won't need all this..it would be pretty easy to create a script that makes a temporary scene with all objects in other scenes linked to it (and rig it so that it wouldn't be exported). It would be a snapshot moment though, as adding new objects to other scenes wouldn't be reflected in it until the script was run again.
You can then get rid of that scene by just removing it.
Also I agree with the idea of keeping the 'page_num' property legacy to overwride the scenes system; this way people can use whatever method they prefer. (as long it's not a source of export issues or bugs)