Napoleon: Total War doesn't change much, however it delivers fantastically. I am deeply impressed with what CA has done.
Which, is my favorite new feature, liberating. Instead of having to worry about rebellions and the people's favor, you get a new trade partner and ally as a protectorate. Also, the supply depots make replenishing troops less of a hassle. You don't have to auto-replenish after every battle.
The Napoleon battles from Italy to Waterloo add some change to the game, much like Independence did in Empire, that stray from the Grand Campaign. They are good campaigns and I enjoyed them, however their replayability is lacking.
As always, mods will make this game truly shine. There are already startpos mods to allow you play as any starting faction OR emergent faction. For example, you can do a Grand Campaign as Scotland or Greece and take on the fury of the Napoleonic Era in a totally unique and new light.
All in all, I think this game improves on the fundamentals of Empire, which was the riskiest Total War made yet, but it definitely delivers where the Empire launch did not. It might not be a whole lot different from Empire 1.5, but what it changes is stellar and what it offers is amazing.