Medieval II is hands down the best Total War game in the Series. My only real complaints are that the AI never seems to be able to counter my Hannibal style double double-envelopment, Offensive sieges are a joke, auto battle is the only sane response, and it feels pretty unrealistic to conquer most of Europe.
I would agree with Yellowjacket about scale. In Medieval as Scotland I managed to win a long campaign by 1306. In Crusader Kings II playing Dunkeld, I managed to create the British Empire and control the modern day UK-Ireland plus most of Netherlands and parts of Austria at the end of the game in 1453. And that was after carefully managing the Scottish realm, putting down countless rebellions and nibbling new lands.
Grabbing new lands in CKII is a long and sometime painful process with fabricating claims, marriages, and costly in golf. What's worse the nobles you now gained hates you, the peasants could potentially hate you if you are the wrong religion/culture.
Choosing between Crusader Kings II and Medieval II, I have to say Crusader Kings II is personally the game I enjoy more. (Oh yeah, CKII Game of Thrones Mod, The King in the North!)
I'm eagerly awaiting Rome II Total War two and Mount and Blade II: Bannerlords. My ultimate game would be the battlefield fighting system of Mount and Blade, the battle system of Total War, and the Dynastic system of Crusader Kings II, that would literally ruin my life, I would never leave my PC ever again...