So I've spent a bit of time playing the Napoleon... I think how I feel about it can be best described by saying that It is Windows 7 and Empire is Vista. There is such a myriad of small changes, they add up to a much nicer experience. On top of this, I don't know if its just me, but the game just runs incredibly smoothly. Battle AI finally seem to use a good level of common sense now too! (finally >_>) Anyway, lots of changes like:
 

• New user interface which so far feels pretty good.
• Engine optimisation
• Decent weather system
• New system of attrition
• New set of vocals for units (some nice pain ones)
• Better visuals all round (fog, unit animation, terrain deformation slightly better, scenery)
• More responsive unit control

Oh man I totally forgot about sea battles (when I run a country, im not very seafaring!). Is it just me or do they let you zoom closer in on the ships now? I dont know but they just look way nicer? 
 
Oh and there are already a few mods that fix things that arent great. Like, theres a musket sound mod, that changes it from *poof!* to *crack!* sort of sounds, smoke mod will probably come soon too (it fades way too fast).

Like I said I'm not very familiar with the Total War series. I almost didn't play any of the previous games at all. But from being mostly familiar with Napoleon and having played sea battles quite a few times now (cause its so damn hard and I never give up) I definitely agree. When zooming in on a ship it looks really good! Generally the zoom in the game is pretty awesome.

There are mods already? I hadn't even thought of modifying the game yet. I think it is great the way it is originally. But yeah, the smoke from the gunfire fades away too fast. Also, I'm not quite sure, but I cant seem to remember there being too much smoke appearing during sea battles. I know its only natural that the smoke fades away faster on sea than on land. But still, it would be awesome with a more visible smoke layer during the sea battles when ships are firing like crazy. Anywayz, I will definitely check out some mods. Perhaps I'll find something that suits me.

I agree, the UI has been changed to the better, and lots and lots of small good changes overall to the game. It still doesn't seem like as full of a game as Empire though, which I guess is intended since Napoleon is cheaper on Steam than Empire even though it's older. The tech tree seems kind of limited in this version, though I haven't played more than a few hours of the first campaign yet.