I'll second this. With loads of scripted events, branching paths, characters moving around, etc. Would be much closer to the fire emblem feel than a TW game.
In fact, I believe Kaga is working on such a game as we speak, related to his Vesteria saga games. Hopefully we will see an english release.
As for total war itself, I see the fates setting as probably the best bet, with its main issue being the distaste people have for it due to how it was presented in the actual 3ds games.
However, you have probably the best instance of visually and musically unique factions, and units that are just different enough. Whereas other games have nations using the same units, or are "the pegasus knight kingdom" or otherwise defined by a single unit. Looking at mercenary vs samurai, for instance, it's clear that mercenaries get more HP and defence, while samurai are built more around speed. This would translate very easily into giving samurai higher melee attack and movespeed and giving mercenaries better armor and melee defence. Since most of the units in fates are mirrored-yet-different in this way, you could have two factions that may share some similarities, but play quite differently. Plus you could get stuff like faceless, stoneborn, and the history guys would really love 140-man regiments of Butlers.
Unit promotions and having greater variety at the top end worked fine in Shogun 2. You could do something like have Cavaliers be all-around light cavalry, with Paladins as an elite fast cavalry and Great knights as heavy cavalry. 3 different units.
As for everything else, most of what was probably thought impossible has been shown to be doable by the total warhammer with its dragons and fliers and monstrous infantry. Personally I don't dig the hero units but they wouldn't be out of place.
Honestly, from a design standpoint, it would work well, the main issue is probably a lack of interest between the communities. I don't even think you could find people who would make a mod for this. You'd need somebody like the guy who has been working on hyrule total war for the last (12 now?) years.