My preference would be to cover the material with three articles.  I think the main Fullmetal Alchemist should be kept basically as it is now, covering both the manga and the franchise as a whole, with the details of the anime separate.  However, I don't think it makes sense to combine the first anime and Brotherhood into one article, as they are separate series with divergent plots, different reception, different production staff, etc.  So my preference would be to have a separate article on each of them.  I think there would be enough to write about that there could be separate articles about each of the two anime series.