Empire is the 'better' game, theres much more to do with a campaign spread over 100 years, 200 turns and one of the most influential periods of human history. If you like the American war of Independence theres a tutorial about that (although I find it a bit preachy and flag waving). Of course the opportunity to learn history is a bit diminished as from 1700 your path, and every other nations spreads out.
Speaking as someone who has both, I'd say if you were bored buy Napoleon, the gameplay is better, not drastically, just more polished and improved. The campaign no longer stretches across half the globe, now its an even smaller version of Europe. North Arfica, Turkey and the Middle East have been removed but the end product is much better. More provinces means enemies are harder to beat (in Empire, you can beat France quite quickly as they have only 2 provinces in home region and start with no garrisons) while the permanent generals feature means important characters such as Wellington, Napoleon and Blucher cannot die so long as their faction survives, they just spend a couple of turns out of action at the capital. Since these are your best generals they will often clash several times, giving these Generals their own little story and notable encounters.
Empire is quite big and in some places unfinished, large areas of Canada and America are classed as 'Wasteland' you can't conquer them, build roads on them or really do anything about them. However, some Native American factions require a very long trip through these areas to reach. It really is annoying to look at the map of America and see large areas of grey as it looks like the developers ran out of inspiration as they went further west. Oh yes, Switzerland doesn't exist because of this either.
Diplomacy in Empire is more annoying the more you play. Playing as the British for example, conquering parts of America and India are important, however, the more you conquer the more other factions hate you. Every province you conquer giver other factions a -6 penalty against you. Doesn't soud big but on the scale of Empire when you start with +60 with your best friends they will hate you by 1720. Napoleon fixes this and its possible to have good friends as you conquer across Europe.
Oh dear, I've talked for ages, I'd reccommend Napoleon, you like that era very much. But if you want a game to give you so much to do that 200 hours will need to be set aside get Empire.
Or get another £2 and buy both, thats the best option.
