You know... it'd be an awesome addition if Shogun 2 featured 1-1 combat with the various generals / famous samurais similar to what Koei does with their "war games". If you ever study the Warring-States period in Japan, you hear all these tales about famous duels. It'd be awesome if you can initiate 1-1 duel against enemy commander/generals, and dramatically shift the on-field morale. There's definitely balancing issue (cheap way to decimate superior force), but if they tweak it right, it'd be really interesting addition to the combat system. The whole commander bonus mechanic is getting stale, and this would reward risky plays with commander units even more.
Otherwise, I don't think I can stand another melee-style Total War even with Shogun period. At least with Musket/Gun era, there's more to explore in terms of logistics and industry if not in the battlefield. Oh and they really need to restrict the movement of armies off of roads if they're keeping the Empire's production site mechanic. It's really frustrating having to guard every little mines with 3-4 units just to prevent 1 unit army harass.
I also think that Empire/Napoleon wasn't as interesting (at least for me), was simply due to scale & realism. The combat mechanic of musket, I think, requires much larger armies to be interesting. along with more realistic handicap. For example, unit order have delays in execution if they are further away from commanders (not just for morale boost). This way, deployment formation isn't simply about how wide you can spread your infantry and how well you space out the artillery/calvary coverage. And if they can pull off the scaling, ala Supreme Commander, that would be awesome. You might want to re-tweak the mechanic and slow down the pacing, but wouldn't it be great to have an actual Battle of Waterloo in 1:1 scale?