Guys, Bones did not up and decide to ruin a beautiful manga. They got the series when it wasn't very far into the manga, and it was only publishing once per month. They must have known from the start they'd have to split from canon at some point. Did they do a brilliant job of it? Well, no. But they did not set out to ruin your perfect story, nor did they deliberately screw it all up. They were operating under external constraints that forced them into rather less than ideal situations.
You want to see an anime that might as well have deliberately set out to screw things up? Go look at Bleach, its slipshod pacing, its rough insertion of characters in the wrong places, its careless cutting of important moments--when it had plenty to work with in the start.
FMA simply did not have that luxury. It would have been nice if they'd waited to license it until the manga was finished, but as things turned out, that wasn't what happened--so they had to stumble along with their own plot. It was nowhere near as good as it could/should have been, but to a point they did pretty damn well. They fleshed out a bunch of minor characters, captured several scenes beautifully, and in general gave us some excellent moments and a reasonably decent plot for a while.
It may not be the manga, and it may not be what you wanted, and it may not be everybody's cup of tea, but stop acting as if Bones is the Antichrist because they couldn't live up to the manga.