Returning to the setting that got the series its start, Shogun 2 is just like the recent-ish Medieval 2, in that it's basically a remake of an older Total War game, dragging its technology and gameplay into the present day.
Because Japan isn't as big as well, half the world, the scale the game loses in comparison to Empire: Total War is compensated for by a return to "story", with the relationships between warring Shoguns of great importance, along with the addition of "hero" units. It also marks a return to the days of you directly entering the game, as your character can be moved around the map, which can be both an influence and a danger.
All that work that went into naval battles in Empire and Napoleon is also being retained, with ship-to-ship combat featuring.
Most striking to me, however, is the game's art direction, which eschews the "classical" paintings of recent games in favour of a crisp, Japanese style.