In some ways I agree with duckroll, in others I don't. I'm kind of in a unique minority.
I don't think Brotherhood is great. I don't think it's terrible either. I'm still watching and it's an enjoyable show. But enjoyable on the level of say Naruto or Bleach anime. Aka, outside of the plot, the animation itself is terribly generic.
Anyhow that's not why I'm in a minority. A lot of people dislike Brotherhood because they think it does a poor job at bringing the manga to screen in a way that does it justice. I disagree, I think the manga isn't very good in the first place and that along with the lack of good direction makes the show very average and forgettable.
There are a couple of things Bones did with the original series that elevates it into one of the top10 anime of all time:*
1) Mizushima. While Mizushima did direct the terrible Gundam OO S2, outside of that Mizushima has proven himself several times that he is an incredibly talented director with a great sense of unique style and overall plot direction.
There is absolutely nothing in the new anime that compares to the Ed vs. Greed fight in the original FMA series. That fight oozed with style and had incredible animation. Same thing with Ed vs. Wrath in the finale, or Mustang vs. Pride with snap snap snap snap snap after the horrible gut-wrenching death of Selim. Then the way he directed Ishval, and finally the finale. The last episode of the show was one of the greatest anime episodes ever made and was 100% original material.
Which leads to the other aspect,
2) The original story. Personally, I think FMA is the most overrated manga in history. It had a fantastic premise, great characters, but after about 70% in (around Briggs) the plot got really dumb, generic, and wasted the opportunity of having all these great characters. It forgot some characters it had built up even existed and ditched all the interesting setups of main mysteries left in the plot with boring or non-answers. Now there's still 3 chapters left, so maybe it will change things around, but as of now I think the manga is a failure similar to 21st Century Boys. Great setup, exciting read, but can't close the deal and deliver a good finish. I actually find FMA worse because it setups up a huge complex epic story, and ends up being a really simple short story that only took so many years to finish because of the slow monthly releases and padding.
Sure the anime plot has some BAD SHIT like ROBOMAN or lame Wrath and Sloth. But the way Bones took the mystery of the door and alchemy and the build up of characters like Scar, Mustang, etc...and wrote their own story was fantastic. They created a deep and interesting tale with an extremely satisfying finale (let's not talk about the movie version; the movie was plain terrible.), the endgame twist of linking it to the real world worked very well. Yes, the anime had pacing issues for the first 15 or so eps, but for the bulk of the show it was well paced and even some of the later episodic filler like the Lust village trip ep were good.
So without a great director at the helm and stuck to a plot that is less than stellar, brotherhood really never had a chance to be anything more than an "ok" show. Like the manga, it's entertaining but ultimately an empty experience.
*According to gaf best anime thread