Here is my take on the two series. First of all, both of them are great and each a masterpiece in its own right. But at the same time, they cannot be more different.
Brotherhood, as most should know by now, follows the manga almost panel to panel, though there are a couple of differences.
In terms of the story, because at the time when the original anime was being produced, they only had a couple of volumes worth of material to work with, so roughly the first 25 episodes of the anime was dedicated to those volumes and they aren't completely faithful adaption either, as many fillers were added. The production team obviously didn't want to add more characters as they had little episodes left to introduce them, so they took what intended in the manga as a subplot/theme, namely the creation of the philosopher stone and human transmutation and developed into a full fledged story. They had to change the nature of some of the antagonists as well as the subsequent ending as a result. The story is dark, edgy, and totally heart wrenching. If you like stories without a lot of angst, this is the exact thing for you.
Brotherhood on the other hand sped through the introduction episodes in order to get to the new material. No filler story was added, and even some of the stories in the first volume of the manga were cut out, only the essential parts crucial to the overall plot were kept. For those who have never seen the original anime, they would have little problem with the pacing. But for longtime FMA fans like myself, it probably felt very rushed. That being said, I do understand why they did that, they are on a pretty tight schedule to tell a story as complex as Brotherhood with limited budget. The journey still starts with the Elric brothers since they are the main characters, but the central plot by no means evolves around them. In a way, they weren’t even supposed to be part of the scheme until they dug their nose in the philosopher stone business. In other words, the whole conspiracy was brewing even before they got themselves involved. There are so just many subplots, all with common threads tied to the final revelation, which doesn’t really occur until episode 45ish, allowing the momentum to build up. Brotherhood has a much larger cast than FMA, and every character has its place in the story, each with their own unique background and significance. To me, the plot definitely better organized than FMA. The author obviously knew exactly what she was doing ever since chapter one because she drops hints here and there throughout the story, and if you think hard enough, you might just figure out the clues before they are revealed.
As you can tell...lol..I'm partial to Brotherhood. I do love FMA as well, but the show left me feeling a little blue and dejected. Brotherhood has its angsty moments, but it also inspires people to have hope. I really loved the way moral themes are explored in the story. Even though all the loose ends are tied up neatly in the end, it wasn't done in a way that leaves little space for thought, in fact, I finished the series contemplating the very nature of humans and our relationship to one another. I recommend both versions~
Sorry for the long rant lol