Pssst. This is BONES. Chances are they'll deviate from the manga's plot in every way possible, maybe quite early on.
They may have fucked up a bit with FMA, which, IMHO, doesn't compare too well to its manga, but Darker than Black apparently has some manga still being published as well, and that one doesn't seem to measure up to Bones' take with the anime, from what I read of it.
Let us hope they continue with this trend.