For strategic (empire-level) AI:
Galactic Civilizations 2 wins that prize hands-down, especially with both expansion packs. The computer-controlled races are pretty damned good -- sometimes, almost frighteningly so -- at reacting to the other races' plans and exploiting weaknesses (including my own).
Honorable mentions: Sword of the Stars (Complete Edition) and Gary Grigsby's War Between the States.
For tactical (combat) AI:
Shogun Total War retains the top spot in my personal list of games. I've generally found it to be a competent opponent, and has in fact wiped the floor with me on any number of occasions. The AI's only real weakness (at least that I've noticed) is that it tends to be a bit reckless with its generals. Otherwise, however, it's awfully damned good.
Honorable mentions: Medieval Total War (the original) and Sins of a Solar Empire.
EDIT - Oh man, Total War AI? Oh dear. These are the games where single province nations will declare war on giant neighbours they had a treaty with for no reason other than 'diplomacy engine' = 'kill the player'. On hardest it's cheating to all hell too, and it's STILL hopeless.
Sadly, I must agree. Even in my beloved Shogun and Medieval, the strategic AI has always been somewhat weak, and this problem was only exacerbated in later games with the introduction of the 3D campaign map.
Also, as you've already pointed out, diplomacy throughout virtually the entire series has been broken. It wasn't *quite* so bad in Shogun (as it was, in fact, rather common during the Sengoku Jidai period for the various clans to betray each other at some point), but diplomacy been vritually meaningless in every other TW title since then -- and it should be a major factor.