Brotherhood with the DLC is my favourite single player Assassins Creed experience.
For all the talk of a general lack of polish, I'm actually rather enjoying AssCreed 3. So far the only oddities I've encountered are:
1) A floating apple
2) A small fence launching me almost 100m into the air and thus causing me to fall to my death
3) A female NPC becoming one with a large wooden pole. No, no, get your mind out of the gutter -- it was she who was stuck in it.
4) Liberation
contacts (the game says "contracts" but I assume that's a typo... one of many) not always being in their respective designated areas
5) NPCs suddenly disappearing right before my eyes. I assume this is due to the game's maximum NPC count, but previous entries handle the culling in a less obvious manner -- 3 seems to remove NPCs from sight with no concern for the camera position.
Edit: As mentioned earlier, the original, notwithstanding its flaws, is still my favourite.