What's the advantage to "everything in one folder"? I'm missing something here.
backup purposes primarily. and no chasing down long directory trees to mass delete saved games through the OS (ever tried to delete a couple hundred savegames in skyrim from inside skyrim?).
and yes at the moment, the game just uses current working dir, no specific paths. so you can install and it works anywhere (well, at least anywhere UAC allows). this also means you can freely move the game folder without breaking anything. however, such a setup does not take user permission systems into account. i remember first noticing way back at OSU (late 80's) that such a setup is really not the UNIX permissions way of doing things.
Things like backup actually becomes easier if everyone plays by the rules and stores things in (roughly) the correct place, As a user i don't want to keep backups of all my installed games (doing so would require insane amounts of space and re-installing them from disc/steam/gog or a downloaded installer is trivial) and i definitely don't want to set my backup scripts to make backups of C:\Program Files\game1\saves , C:\publisherX\game2\saves, D:\game3\saves, etc
If all applications behave as they should i only need to make a backup of the user folder and everything that can't be re-installed will be covered (documents, photos, code, save games, settings, my browser bookmarks, etc, etc), if i use network/domain user accounts (or just store the user folders on a NAS and configure the local users on all machines to use that) i can share all that stuff between all my machines seamlessly while still having all the big game assets, binaries, etc on a local SSD on each machine for fast loading.