The Brotherhood style adapts the art of Hiromu Arakawa better than the style of the first series. I'm a big fan of Arakawas art, it's quite unique. In Fma 1 they had a more mainstream-friendly stlye. Fma1 looked like just any other Anime. The usual pointed chins, every guy turned into a bishonen. And everyone. Looks. The same.
But there are some things, that bothered me REALLY much even before there was a FMA:B:
- Eds Bangs. THAT:

Seriously, what's up with his hair? what kind of hair falls that way? It was like that all the time. I always wanted to jump into the screen just to correct his hair. And beat the fanartists up who do it like that as well.
- Als Hair & eye color.
ew. Who thought that Al had this ugly shade of blond? It's almost brown. Ed and Al have the same hair and eye color. Always had. Always will have.
- Hohenheim
Who is this guy? In fma1 there is someone else posing as Hohenheim. He has no resemblance to the real Hohenheim. Hair and eye color are different, facial features are different, his hairstyle is different, his nose, his beard. And the look on his face. He always looks like he's falling asleep any moment.
- the NOSES
Are. Too. Long. Their faces look so long, and since everone has the same nose there is no characteristic about it.
- the facial features...or the lack thereof
They all have the same face minus the size and color of their eyes and their hair. If you would remove them, everyone would have the very same face.
now on to FMA:B:
The colored outlines of Eds, als and Hohos hair was a bit weird for me as well at the beginning. But I got used to it. However, what I don't like about Eds hair:
- His braid
It's too...fluffy?
- the length of his hair
or the inconsistency of it. In one episode it's rather short in the next one it's way longer. you can see that especially well in the period of time between um I think episode 44 and 45. it grew...a lot.
- his bangs from time to time
they look really weird sometimes. too lazy to get a screenshot, but when he was in hospital after lab 5 (dunno which episode it was) his bangs looked...really...weird. Too spiky... divided strangely.
Brotherhood has some flaws here and there, but it's not like there weren't any in the first series. overall I like fma:b more, obviously. Maybe I'm biased, because I read the manga even before I watched fma 1. But seriously, fma 1's style of art looks like any other anime. It's really unoriginal and hiromus artwork was adapted rather poorly.