Has it though? How often has an anime set forth to do something different to the original source material and I don't mean filler arcs because you've run out of material, or brand new endings, or weird pacing. I mean actually tell it's own story in it's own way. Plenty of shows created by less than talented staff turn out badly but I don't think that means anything for the very idea of making something different from the magna.
The original Fullmetal Alchemist isn't just a straight adaptation with a different final act, it's re-writes on the story throughout, inserts brand new material, expands upon existing material and completely re-arranges the way revelations are delivered to the audience. In the original manga, there's no explanation of the boys origin until Volume 5, that's after Nina, after Scar, after Hughes. The original anime series moves that right to the start of the show to create a core emotional and thematic base of the series and it's a great decision that completely changes how you view the series right from the beginning.
There are other examples too, think of K-On! which started out as a simple 4-koma gag strip. By the the time KyoAni have made the second season the show was completely different to the manga. Or think about how they decided to change the chronology of the storytelling when they made Haruhi.
When creators think about the unique position they're in when it comes to adapting a work into a completely different medium and understand the mediums strengths and weaknesses they can produce great, new works, not simple re-hashes of stories that already exist in a different form.
