I think you guys have changed my mind. Templates and unique abilities don't need to be in a book at all, because either one can be added on the fly, as-needed.
To borrow an example from my home game: If I need a troll that fights with a ship anchor and chain, and uses it like a giant grappling hook to snare/capsize the escaping lifeboats of sinking ships, I don't need full stats for a "Harbor Troll" from a book. I don't need to create and apply a "Harbor Monster" template, either. I can just make something up in the moment and run with it.
I guess I'd put this under the "Rulings, not Rules" umbrella. A sidebar in the Monster Manual about how the DM might customize/create a creature, along with an example or three, would be far more useful than a new book or game mechanic.