Great game, must buy if you like Total War
Empire also suffered from having some fairly boring battles. Unless you played online, the AI was usually not a suitable foe and the terrain was bland.
Napoleon Total War pretty much fixes everything I disliked about Empire. The bugs are pretty much gone (save for some annoying pathfinding and command issues), the AI is somewhat more aggressive and reactive (though still not a great challenge) and the new focus on terrain makes battles more interesting.
The Grand Campaign of Empire was for the first few weeks impossible to play, though after the patches it was as fun and immersive as the other Total War titles. Napoleon's truncated campaigns (for Bonaparte) are fun, but are very limited in scope. There is a similar type of Grand campaign that focuses on the nations allied against Napoleon, but again, the choices are slim as you can only choose a few factions and the action is limited to Europe.
Battles in Napoleon require more maneuvering and attention to position than Empire. This is my favorite aspect of Napoleon. The terrain is more varied, offers more options for the tactician, and can make or break a battle.
Take too long to take the high ground and you will more than likely have to slog it out with the AI.
Also, artillery is more effective in Napoleon. Cannons, howitzers, etc can decimate enemy companies rather quickly if they are caught in the open. Explosive shells are brutal against anything and everything.
So to basically sum up, Napoleon is what Empire should have been. More detail, better battles, a wide variety of extras to keep you busy...it is a step above Empire. The only thing keeping Napoleon from being the next best Total War (up there with Rome) is the lack of Napoleon's Grand Campaign.