These are just my three things, and there are more than three. But in light of such negativity, I thought it would be nice to add the other side of the coin: Those surprising things added to the game that take M&B to the next level. I've got critiques, too, but some of the features added to the game have really improved it for the better.
[list type=decimal]
[*]
The Music - The music for this game is excellent, really evokes good feelings. When I went to a monastery, the holy choir came in right on cue. Definitely enjoyable, suggestive of the time period while also being modern.
[*]
Your Refuge - This is absolutely brilliant, and I squealed with delight (unabashedly girlishly) the first time I realized I could store some stuff in a chest of drawers inside the dingy little shack. Being able to garrison men without having to go through the process of vassalage was also very cool. I can wander the countryside, collect men, and bring them back to my garrison--which trains them as well. It's just an excellent way of adding player housing to the game.
[*]
Owning ships - A huge improvement from Native. Being able to fight at sea, choose your ship, build it, micromanage who/what gets on your ship, etc. This has made trading for me a lot more fun, even though we're at an early age at which the idea of being a 'merchant prince' didn't really exist yet.
[/list]
Feel free to add your own 'top 3' things.