I prefer Brotherhood.
For one thing, the ability to create a homunculus and have it look like someone you know is impossible. The homunculi already made come from one source, the Dwarf from the flask a.k.a Father. When he separated all the seven deadly sins of man from himself, each with a philosopher stone as their heart.
Also, after Maes Hughes is killed, the search to find his killer and figure out the motives becomes how Mustang and his group become active against the rest of the military. I like versus the first anime, many of them like Kain Fury, Hymens Breta, and especially Jean Havoc are made to be seen as more serious guys, rather than just idiots. Jean Havoc shows off his skills as a secret op with The Hawk's Eye in her targeting position. This worked to recover the human body that once belonged to Barry the Chopper.
I also like animes with overall pictures. What was the need for the war in Ishval, or the up-rise in Lior? Is it just to make Philosopher stones? The truth is those wars were just small parts of a great big picture. Like the size of this circle country, Amestris. Central gets its name for being the center point of the country. Father is having his strongest homunculus carve a giant cave circumferencing the whole country to channel the energy needed for his master plan. This task wouldn't be a overnighter, but rather it started right after the fall of Xerxes. Perhaps this had to span 400 years because it was so big. I also like the counter to this major scheme. Hohenheim, among others opposed to it, work as rebels against such pending doom. One of the counters include using alkahestry to not only cancel out alchemy, but reverse it's damaging flow.
Also Ed and Al aren't seen as killers at all. They truly regard all forms of life and don't seek a need to destroy anyone. They didn't kill anyone accidentally, like Majhal or Greed, or intentionally, like the first Sloth (Trisha Elric). Edward even went out of his way to save Selim/Pride's life, even though he ended up reducing Pride to the form of a fetus-sized infant. After learning about Maes' death, Al refuses to allow anyone else to be killed, not while under his watch. Nobody can convince him to just leave them to die. Riza tried that when she thought Mustang was dead. That option was thrown out immediately.