Eh, Napoleon was far better than Empire, and as for some ********-ness that should have been easily fixable (ie not forming lines and melee cluster




) were fixed by a few mods. I actually like the battles, and I think the main part of bad AI in ETW and NTW were the guns. M2TW AI got improved quite a bit with mods so I have nothing to complain about (its still bad but so is Civ AI)
But the point of the OP was what we could take from the TW series, not what Firaxis could take from CA. I would also like to add another line to the purpose of the OP. "what we could take from the TW series and have it still maintain the essence of Civ"
That means no real time battles. Sure, I would love a Civ/TW merge with good AI and little bugs, but in the real world that will not happen. TW battles take long too, and many of us simply do not have the time. Instead, if we want we can play TW and Civ and another game that is essentially Civ and TW, but Civ title itself should definitely not be merged with TW.
Somethings I think we could take is from the diplomacy. In Civ 4 it seems that friends from 4000 years ago are friends for ever, while relations were more unstable in TW. IMO unstable relationship would add spice to the game, and also eliminate how if I dont become a Buddhist, Isabella will still remember that from 3000 years ago. It would take away a lot of the late game boredom as those wars would mean that even if you did eliminate your enemy 1000 years ago and there is only peace, relations could quickly decline with your ally and he will become your new enemy.
Also the importance of the navy in ETW and NTW. In Civ and M2TW and older TW games, having a massive navy as England barely meant a thing until way late in the game, because they can simply load and unload without ever needing to combat your ships. In ETW and NTW units get the option to engage if something gets within the zone of control, so if I have a big navy I am pretty much safe on the island. Also how you can simply raid trade routes, not the port itself. NTW and Civ 4 lets you stop routes by going on top of the road for Civ or holding a choke point the route goes through in NTW, and in Civ 4 it may be near impossible due to road spam but in Civ 5 that wont be a problem. However, unlike in NTW you cant profit off of that, so that should be added