Brotherhood had a lot of good changes, but I agree, the combat was the best one.
I think in order my favorites would be...
I have a feeling AC3 will be my second favorite.:P
So I'm still on my quest to beat all of the Assassin's Creed games before the release of ACIII, and in doing so, I've started new 3rd game, Brotherhood.
Right off the bat I notice a few, subtle, but very nice changes to the gameplay. The most prominent of the group would have to be combat mechanics. In this game, you can easily tear apart groups of 50+ guards all at once. Those who've played both of it's predecessors know that the first game incorporated great counter maneuvers which made for pretty good combat on the lower side of enemy numbers, but once the enemies elevated anywhere past 10 - 15, the combat would become slightly redundant: You attack, get off one or two nice counter moves, and then bam, sliced in the back multiple times while being ping-ponged back and forth between enemies.
In the second game, however, they managed to improve upon the combat system, but it didn't feel entirely the same. More of this game was centered around raw attacks rather than visually pleasing counter maneuvers, however, the combat did seem smoother, and they managed to implement a lot of new moves along with the addition of the weapon wheel, smoke bombs, and health potions.
Finally, this time around they managed to effectively combine combat systems to get a finished product that is loads of fun, and completely reflects both systems. You can literally tear through tons and tons of soldiers all in one fight, and you'll find yourself competing with loads of friends to see who can get the best combo multiplier. Now, everybody isn't just a one hit kill; you have to first kill somebody to get a little momentum going, but once you first kill somebody, combos are brilliant fun so long as you can keep them going.
The second most notable change, to me, is the definite movement of Ezio. The character movement seems much more realistic and heavy. If you're running in one direction, you can't just turn around with seemingly no penalty or even a slight momentum shift, you have to actually stop running first. When I say he feels heavier, I don't mean that he's slower by any means, you still leap across the city effortlessly, but you just feel more like a human.
That'll conclude this blog, however, I should also include one more notable thing about the game thus far: It literally starts RIGHT where ACII left off (with Altair's robes and everything), and to me, that give series playthroughs so much more value. It makes it the series a lot more playable. So far, I'm very impressed.