From what I can tell, you can pick which block you take your sites from. Doesn't matter which block (Fellowship, Towers, or King), but all the sites you pick have to be from the same block.
Which honestly isn't a whole lot better (though it is definitely an upgrade). What I'd like to see is a complete rebalance of each site from each block to make them more like the Shadows path, but with a Region number as well (as I've seen suggested here and there), so you'd have a Shadow number of 0-3, a Region number of 1-3, and rebalanced text (such as what was done for Bridge of Khazad-dum, though perhaps not quite as vicious with the nerf-bat).
I think I'd leave the sanctuary keyword in, though, and make it so only sanctuaries can be played at site 3 and 6, which anchors the path somewhat and prevents things like
Steward's Tomb at site 6.
So that gives us a system that's firmly between the rigid Movie system and the overly-flexible Shadows path. A system such as this would have players picking a 2 Region 1's, a Sanctuary 3, 2 Region 2's, a Sanctuary 6, and 3 Region 3's.
This would avoid problems with cards that were balanced around being only played at certain parts of the site path (especially site 9's), while making things more interesting strategy-wise. Limiting particular sites to a particular region would also keep sites from being too weak--if you don't have to worry about site X being played in the first two regions, you can be a little more lenient in how powerful it is.