The FMA fandom that existed on LJ/DW when I got into it was basically ALL about manga or Brotherhood (just b/c those were the ones people were getting caught up on the time) so I didn't see the conflict until I ran into it on tumblr.

And yeah, I can see those ship differences. I've also heard first anime was more femslashy (I haven't actually seen that much of it), with Winry & Scieska hanging out more.