I had a lot of problems in battles, the most obvious being the 'melee bug' (somewhat of a misnomer, it's where the AI can't make a proper line, so keeps moving units forward, eventually running into melee with the player's line).
Also, the Marathas became world powers in almost every game I have played. You could be giving the Persians/Ottomans hundreds of thousands of money (I forget the unit) per turn and every tech under the sun and they will still lose. It is because the Indian provinces are extremely rich. But to nerf them, CA removed their ability to rank fire, making the Marathas pretty boring to play with.
I have heard good things about Shogun 2. Thankfully they got rid of the sheer stupidity that allowed units to reinforce anywhere in the world (reinforce a nearly destroyed unit of Highlanders in the middle of Mexico, sure why not?).