Having played both, I can honestly say that Empire was a much more fun experience for me. Most of its game breaking bugs are gone, meaning you can enjoy a very long campaign without difficulties (most of the time).
What I value in Total War games is high content, less bugs and for the game to just feel right. Empire just clicked with me and seemed like a realistic 1700s battle while Napoleon just felt odd, along with its lack of content. People often say that Napoleons graphics are better but to me, they seem more cartoony then Empires. One thing I have to give to Napoleon though is that it runs amazingly better on my pc than Empire.
One last problem with Napoleon is that it feels like its holding your hand all the way through it, there are many mini French campaigns and one kinda big campaign where you can play as Napoleon's foes. There is no Grand campaign like in Empire and there is no access to America, nor India. Empire let you do whatever the heck you wished, Napoleon greatly limits you.
Empire Total War has much better gameplay. Napoleon Total War focuses only on Europe while Empire Total War allows you to build a global empire. NTW may have better graphics but its gameplay is not as good as that of ETW. NTW gives you an unrealistic perspective of the Napoleonic Wars while Empire Total War gives you a realistic sense of diplomacy and building an empire during the 1700's.
Personally, I believe that Napoleon Total War is much more streamlined. Also, the feel of battles in Napoleon Total War is superior. For example, in Empire Total War I was plagued with units simply not responding to commands as I would expect them. Furthermore, the diplomacy in Napoleon Total War is much better than diplomacy in Empire Total War. The AI in Napoleon Total War also seems slightly more intelligent, and the graphics are far better than Empire Total War.