Why the TW hate? (or something to that effect)
In general, the Warscape engine (I think that's what it is called) was a step back in one major regard: the lack of modding capability. Mods like Stainless Steel, Broken Crescent, Third Age, etc are impossible.
Napoleon was frankly the game Empire should have been. The fact that we were charged another $50 for it was insulting IMO. Like artillery finally having an ammunition limit. It was a good game (or better at least), but a waste.
As for Shogun 2, it was much better in many respects. But battles were streamlined to a point of detriment:
A) stamina didn't really seem to play much of a role, there wasn't much difference between fresh or exhausted units
B) fire arrows
C) climbing up walls. Seriously. Maybe medieval Japanese soldiers did climb up castle walls with their bare hands, I don't really know, but I doubt it
D) rock-paper-scissors taken to extreme levels. A unit of katana samurai charging downhill against light cavalry not in formation due to being in the middle of a forest will still get destroyed because horse=uberpowerful against swords.
E) crazy high morale. Ashigaru units will scale walls by hand straight into the waiting swords of elite katana units even when they are down to 30 soldiers
F) For some weird reason one unit of fire-bomb kobayakawas can rip apart half a fleet.
In regards to the strategy/macro level:
A) Extremely low movement ability/levels/whatever for units, especially considering each turn represented three months
B) TW still haven't been able to fix the fact that a player can field entire armies of elite units. Samurai made up a tiny proportion of soldiers on the battlefield. The vast majority of a stack should be peasants. At least Medieval 2 had the unit pool that made players have to wait before recruiting 5 units of feudal knights.
C) Realm divide. Sekigahara wasn't just Tokugawa v Toyotomi, it was Tokugawa, and a few friends, v Toyotomi, and a few friends.
D) Aside from trade, diplomacy was generally useless.
Also, if anyone ever defends Empire, just ask them how much they sold Florida to Marathas for.