I was just reading through to see if I can get an idea of how much would be pre-built vs. needing to be made with a script. Naturally, my mind first considers the menuing system-- any kind of Final Fantasy game has a main menu and various sub-menus accessible from it-- but the exact layout and contents of the menu would vary based on the specific details of the game. For instance, Final Fantasy IV needs 5 characters to be visible; FF V needs a job menu; FF VI needs a skills menu, etc. My point being that while they are all very similar and can probably be built from the same basic parts, the specific form that you end up with would differ based on the need of the game.

Parallel to that, I think the map would be a fairly universal module across games as well. Maps need a width, height, tileset, and of course the data (including probably at least a couple of layers). Several general things populate the map perhaps as additional layers: NPCs, treasure chests, event triggers, warps, animated tiles, layer-priority shifts, diagonal stairways, etc. It seems me that if you get the map powerful and flexible, and then a menu-subsystem.. that's 2/3 of the work right there (the battle engine being the other 1/3, of course).