Since we're in the early stages of organizing AGS as an open-source project, maybe we can learn something from the history of one of the most successful adventure game-related projects, ScummVM. Conveniently, Ars Technica has an article (http://arstechnica.com/gaming/news/2012/01/maniac-tentacle-mindbenders-of-atlantis-how-scummvm-kept-adventure-gaming-alive.ars) about just that.
They also link to some interesting project pages, like the ScummVM Coding Conventions (http://wiki.scummvm.org/index.php/Coding_Conventions) which help ensure platform portability. Those are issues we should probably keep in mind and practices we might want to emulate in a future refactoring.