While I know these will probably never be done (though with their recent push to add new content into Rome 2 it probably should be done) I thought I'd list some stuff I think could make Napoleon a much better and more fleshed out game.
To begin i believe that Empire could be imported into Napoleon as a sort of expansion, or series of expansions like the Empire Divided expansion in Rome 2. While I love Empire, I can understand that Napoleon is a much more polished game in comparison that fixes a few of the issues Empire had.
More or less, this would be a reskin job and this allows them to create extra scenarios like the Peninsular War they implemented in Napoleon.
For example, the Napoleon campaign map is perfect for several of the European wars of the 1700s, such as The War of the Spanish Succession, The War of Austrian Succession and of course the european theatre of the Seven Years War.
This is not all, they could import the Empire maps for North America and India and create mini campaigns based on them.
For example, the French and Indian War and of course the American Revolutionary War (though I believe the former would need a few extra provinces, while the latter might need a new map entirely to focus only on the Thirteen Colonies and not the wider continent).
Then of course they could focus on other localised wars, like the Great Northern War.
For this war I have a few thoughts the devs could do to bring it to life.
1) the campaign map would only be as far south as the Ukraine and as far West as Denmark
2) Sweden gets a special looking standard line infantry unit that has a mix of Musketeers with a Pike block in the middle (in every battalion at least a third of the men were armed with pikes) which gives the Swedes a more Close Combat focus than ranged.
These units take 2 turns to train and come with a pip of experience. This is to show that the Swedes are pretty good soldiers that can win against all odds (throughout the war they fought outnumbered almost 2:1 in most of their battles and still won) but cannot afford to lose a battle as it'll take a while to rebuild your army (a sort of artificial population cap since CA doesn't want to work with population anymore)
3) this standard unit is only recruitable so long as the Swedish king is on the campaign map. If he dies in battle then that line infantry reverts back to standard line infantry armed with muskets and no experience. The reason for this is because the king was the only person who demanded that soldiers should still use Pikes in his army, even though it took longer to train men to use a Pike compared to the musket.
Anyway, these are some thoughts I had that could spice up Napoleon and add more content to it without too many issues, hopefully. Napoleon Total Wars campaign for whatever reason bores me and I think porting over some of the content of Empire into it might make it a better game overall, especially considering that CA are never going to fix Empire.