The AI is very bad even compared to most Total War games, it splits its forces too much both in battle and on the campaign map, sieges are a mess, and there are several bugs. These include that horrible end turn lag that was never fixed and can ruin good campaigns. Units take too long to form up and don't always go exactly where you want them to go.

Then there's the Old Guard who dislike the warscape Engine and see Empire Total War as the beginning of excessive streamlining; these people are upset with 1 v 1 Melee animations, reduced modability, no diseases, the loss of most character traits and attributes, a less complicated building browser, and a dumbed down replenishment system.

Despite its flaws there are still some really great features in the game. The town wealth aspect is awesome, as are the naval battles. Government types, revolutions and ministers were good additions. It's really cool having three theaters of war. Finally, the technology tree was overdue. Unfortunately, though, because of the bugs and a few bad design decisions, the game doesn't hold up to Shogun 2 or Rome/Medieval 2. If had been less buggy and streamlined while still maintaining its strengths, it would have been the best Total War thus far.

TL;DR : Bad A.I, sieges suck, streamlined too much. Had good features but they don't outweigh the problems.