Well, there are three main holes, in the units upgrade paths that have old an modern units on the battlefield at the same time which just does'nt look right
Pikemen an longbowmen running around in the cannon, grenadier, currisars & cavalry era, it just does'nt look right, when things like pikes are fighting modern cavarly or you are bombarding longbows with cannons, it just goes against what people expect the look of combat in that period to be, units that have there basis in the napolonic era are engaged with ones that have there roots back in medieval times, while i know that early gunpowder units existed side by side with these units before eventually replacing them, in game terms longbows an pikes last to long and extend to far forward into the gunpowder age and the gunpowder era just does'nt look quite right as a result.
Solution, Musketmen the current no role, an forgotten unit of the period should replace these units, and have a 25% bonus vs mounted like riflemen, so, longbows, crossbows an pikemen should all upgrade to the early musketmen unit, the result is the unit now has a clear upgrade path from previous units, which in itself will help to bring the poor old forgotten musketmen into the game far more, and the late gunpowder era will be more characterised by cannons, currisars, grenadiers, & musketmen all doing battle, rather than longbows an pikemen, it will give the era a feel more authentic and real to that timeperiod. cavalry with rifles being fighting men with pikes looks a bit naff.
Mounted unit upgrade path, Mounted units have no proper upgrade path past cavalry, the gunship is miles away, the modern day equivalents of cavalry are helicopters which now fill the role of old light cavalry an tanks which are the modern versions of heavy cavalry, in terms of gameplay it would be much better if cavalry could be upgraded to either tanks or gunships, since these are the modern day equivalents of the unit an this would solve the huge gap between cavs an gunships, it's like a riflemen upgrading straight to a mech inf with nothing slotted in between, they need a more viable and shorter upgrade path an allowing them to upgrade to tanks or gunships would solve that.
Last one has already been mentioned a few times, an thats catapults an trebuchets, something like a mortar or early cannon unit should arrive, before cannon proper, or simply move cannons to a earlier teck with an inherant combat penalty which is only removed once steel is discovered, but again trebuchets an catapults running around with grenadiers, etc does not look right for this era.
BTS took a big step from warlords in terms of enhancing the various unit upgrade paths, era's, sailing ship combat which was a weak area before has been done very nicely in BTS, late modern versions of arty an sam infantry have also given the late modern era a proper feel and that era is now fully done justice too, the only thing they really need to sort out now is the gunpowder era, and not so much in terms of big gameplay changes but, bringing the musketmen more into play, so that he bridges the gap between medieval an late gunpowder, he does'nt bridge this gap at the moment since he has no upgrade path from prev units, and this results in to many old style units getting into the later gunpoweder era, which just does'nt look right at all, the trebuchet/cannon issue is also one that needs addressing but these are'nt big things so i dont see why firaxis cant just tweak this in a future patch