This is quite impressive! An only usability detail: why do you need all users to approve access to the file system, if that functionality is only required for saving games? I'm sure most users will be scared by that banner.
That's a Flash problem - you can possibly use more space than the 100k default if you have five profiles, and Flash will fail silenty when trying to write to it unless you ask for the block up front.
And the Flash prompt is pretty badly worded - it's just the Flash cookies that it's talking about!
The whole thing has driven me crazy...
Edit: Oh, I see what you mean about waiting until the user saves. The game saves transparently when you walk around so there's no other good time to pop up with the allocation popup. Would have been much easier if we used a 'choose slot to save' kind of system when you are back at base.