(going to be comparing the campaigns, ignoring multiplayer/historical battles)
It really depends on the experience you're going for. If you're more into the American revolution technology, and the 7 years war era, go for Empire total war, its campaign features a much larger map (I recall Europe, North America, and India as playable pieces), and the mechanics are pretty similar, but Empire total war has a more diplomatic side with the colonies, as you can convince the colonies to not rebel. Empire: Total War is good for a grand strategy lite experience mixed in with RTS.
If you want a European battlefield, go for Napoleon, it features the technology (shockingly) from the Napoleonic wars, and the abilities of your armies reflect that. Do note that the campaign only takes place on Europe. If you want to play as a large power (ie France, Prussia, Britain) I recommend Napoleon.
They're pretty similar games overall, so the main differences are that Napoleon is newer, looks a bit better, and has a few more units in the English and French categories, but Empire has a variety of units and countries.
Also : Napoleon has a head-to-head/co-op(?) campaign, while Empire does not have any multiplayer campaign (despite being promised it)
As for the AI issues that CypherX says, I highly recommend the DarthMod (available for both games), which overhauls the entire game, ensuring a smarter AI and a more enjoyable experience.