I feel like it could work to have a bunch of random teams all over the place... if the game was designed as if Hitchcock planned it. That is, the entire game is designed, all mechanics are pre-planned and thought out (though I've recently discovered this isn't a common skill?) as best as possible, and all that's left is to build and iterate.
AC3 feels like someone went "oh, hey, we want fast travel, so that's your responsibility, get back to us when it's done."
Contrast this with Far Cry 3, which feels very consistent (despite having a significantly larger world, more quests, presumably more AI behaviors, etc) and polished. It feels as though a handful of people got together, planned out how all the gameplay and systems worked together, laid out a genral idea of the missions, and theen developed, allowing for improvisation as they needed.
Granted, Ubisoft's writing teams are almost universally awful, so that threw a wrench into things.