I think a Sootopolis thing in the deep water area would be nice. That is, an island you have to dive underneath to access the middle of. This showcases the underwater transfers. It'd just be a small island, though.
The map-modifying solution I came up with is similar to FL's, except the pictures added are only small parts of a region (no need for pictures that are larger than necessary). The base map is loaded as normal, and the extra parts are layered on top if necessary.
Do all maps in the game always show the same configuration? That is, if I unlock Newmoon Island, does it start showing up in the Poké Centre's wall maps as well as the player's Town Map? I think it wouldn't, and that the wall maps only ever show the base map.