Brotherhood didn't handle the opening episodes as well as the manga, but what it cut at least didn't have a huge impact on the plot (even omitting Yoki's introduction until later on was done well by at least giving nods to him through the newspapers) and I vastly prefer the quality of FMA:B's art to the manga due to not being a fan of Arakawa's thin, light lines in a lot of panels. Overall, I'd say I prefer the anime.
If we're talking about the 2003 version though, then Manga >>>> Anime.