To give it a fair shot, I felt I had to watch it a second time. It's kinda like when I saw the theatrical Pride and Prejudice movie; the first time though, all I could think was "this is not A&E's Pride and Prejudice...this is not A&E's Pride and Prejudice...this is not A&E's Pride and Prejudice...". I wasn't as conscious of doing that with Brotherhood, but still, I felt I should watch it a second time. Forgetting about the first anime, because I really wasn't expecting it to be the first anime and it shouldn't be judged against it, here's some more thoughts:
• I love the opening and ending. Both do a good job of capturing the series.
• The fight scenes are awesome. Al totally rocks, Ed is amazing. Ed losing his temper - really losing it, not his "you called me short!!" flailing - was a great scene.
• The animation, I think, is just going to take getting used to. I wish I could put my finger on what it is about Ed's character design that bugs me, but he just seems off. All the appeal he has in the manga is only sort of hinted at. Same with Roy. Most of the other characters are fine. Kimblee (what we see of him) looks great. Hohenheim looks good. But Ed and Roy bug me.
• I'm still put off by the rapid-fire reveals. It felt more like a story pitch than a premiere. "Look at all our cool characters! See all the nifty stuff they can do! Aren't you intrigued?"
• If I was coming into this not knowing anything about the story, I think I'd be confused as to who the main character is supposed to be. "It's called Fullmetal Alchemist, and that's what they're calling that little guy, but why did it start with that other guy? And who are these other people? Should I care?"
• In the manga, we meet Ed and Al. We don't see any of the military characters until the fouth chapter, and it doesn't spend any time on them until the fifth. It's very clear who our main protagonists are. We get to know them and get to know what they can do, before the story line gets cluttered by the secondary protagonists. In Brotherhood, it's like everyone is given equal weight.
• Roy's introduction is rather shaky, really. In the manga, as soon as we meet him, we know he's sarcastic, would rather be on a date than doing his job, and is perfectly happy to let someone else (Ed) do the hard work, and it's obvious his staff knows better than to take him too seriously. But when he does take action, he's calm, collected, and casually badass. And arrogant, let's not forget. We don't see that he has a major weak point (water) for some time. In Brotherhood, none of this is really established. His weakness is thrown out right at the beginning. He came off more like a sulky teenager trying to act adult. Especially with his "don't underestimate my flames!" screech. Roy shouldn't be losing his cool that easily. We really didn't get to see any of what makes him such a good character in the manga.
• We shouldn't be suspicious of Bradley this soon.
They probably wanted Brotherhood to be distinct from the first anime right off the bat and, unfortunately for them, the first anime follows the manga pretty closely for the first two episodes. But this really didn't strike me as a good solution. It was too muddled, and revealed too much too quickly. It would have been a good story to do maybe three or five episodes in, but not at the beginning.
Edit: On further reflection, it seems like this anime is assuming viewers have already read the manga, which is a strange thing to do. When a story switches medium like this, it should stand on its own.