Beyond the improvement to grapics, and making sieges more fun I found this game to be a huge step backwards from Medieval 2.
The scope of the game is just waaaaaaay smaller. A medieval 2 game could take me weeks to complete, same for Rome:TW, but in shogun I can finish one in a couple of days on the longest setting on the hardest difficulty. (I never played the empire ones since they didn't seem appealing, and from what I read they weren't as good either.)
The improvement to the way buildings are constructed (no more tedious queueing) has actually resulted in more boring gameplay despite being a good change. Why? Because now, instead of waiting for buildings to complete, we get to wait for the stupid tech trees to finish their tech advancements. I've lost count of the number of times where I've sat there pressing NEXT TURN over and over again to get a new advancement I'd need, while my gold piles up to the tens or hundreds of thousands.
The worst part for me, though, is how every single faction is basically identical. The Medieval or Rome games had wildly different factions in wildly different starting locations that played completely differently depending on their religion and units, while in Shogun 2 every faction is basically identical, the only real difference being some very minor differences to basic units. I'm pretty sure I can list every unit in the game off the top of my head right now after playing it for a week, and I've seen every area of the map. In Rome or Medieval, I played the games for months before I even saw half the world map.
Also, the Shogun 2 events are far less interesting than those of medieval. In shogun 2 you randomly get more food or income, in medieval the mongol hordes invade and destroy your entire empire if you're not prepared, and the "realm divide" event is far less interesting (since it's compeltely predictable and does the same thing every time) than having to deal with the pope in Medieval. That guy really had it in for me.
There are also many obnoxious limitations that don't make any sense except from a balancing-perspective, like how units can't be retrained or how disbanding decade old veteran units and training new ones from your, now upgraded, regions results in more experienced units with better equipment (bonus accuracy/morale/armor/weapons). At one point I realized that disbanding my veteran katana samurai and simply replacing them with normal ashugari (with +6 experience, +4 melee attack and +2 armor) resulted in more powerful units at a lower cost...
Overall it's not a bad game, but except for the (admittedly significant) improvements to how the battles look, the game doesn't begin to compare to Rome or Medieval 2, which is pretty disappointing.