I loved brotherhood A LOT more than I did the original, if only because I was reading the manga at roughly the same time and I kept getting confused between what was what. My own fault I suppose. But I still disliked the original in how much it deviated from the original manga, and it just felt like too many other anime out there.
However with Brotherhood, my own qualm is that it didn't put in a lot of the comedic moments I loved in the manga. I kept on going "Ohhhhh! Where's that joke?" Other than that, I loved it through and through and remains firmly in my top 5 anime.