You are DEFINITELY not the only one who still like the first FMA anime. I was just having this discussion with my bestie last night, on account of we watched the whole first season of Brotherhood together (and are both gigantic FMA nerds who would text each other SPAZZING when the last chapters of the manga were coming out).
I think the one difference between the two series that I just can't seem to get over is the visual aspect. I mean, the differences between the plot, the characters, and the antagonists' role in the story can be attributed to a huge pile of different things: the manga wasn't finished yet when the anime was being made and they just had to make s**t up as they went along, and the people who made the anime made different stylistic choices than Arakawa herself would have made when portraying the characters. But this stuff isn't uncommon among anime adaptions to manga. The fact that Brotherhood is an almost EXACT reproduction of the manga is actually more UNCOMMON to find in anime than otherwise.
But again, I return to the visual aspect. I like the anime in Brotherhood, don't get me wrong. It's not ugly by any means. In fact it's quite skillfull. But the animation, the art quality in the first one...oh my GOD. It's a ******** EYEGASM. I just...I've never even HEARD of an anime with as much attention to detail, with as much stylistic DRAMA as the first FMA series. Just watch the first two episodes of the first series, then watch the third episode of Brotherhood, back to back, and you'll see what I mean. Ohmygod. Ohmygod. I still get gleefits of Art Whore whenever I watch the first series. Never gets old, man. Never. Gets. Old.
Allow me to conclude by saying that while I recognize the strengths and weaknesses of both animes, I am a MASSIVE FMA nerd (I mean ********' duh, look at the account I'm posting from), and love both series and the manga equally. And always will. It was the anime that got me INTO anime (yes, I watched DBZ and Sailor Moon on Toonami, but at the time didn't really register that they were ANIME, you know?). It was also a series that boosted my inspiration, and thus by CONSTANT PRACTICE my ability, to write--which is my primary passion in life. I owe a lot to FMA.
So yeah. Haters, they gonna hate.