I really pag-ibig both! I saw FMA Brotherhood before I saw The 03 FMA anime. I did see differences between certain characters in the two versions of the anime. I think it's really good either way. Well the different Wrath's and Sloth's were something..like I loved the 03 Sloth the 09 Sloth not so much But that's just a minor problem. Roy is a little madami loose in FMA Brotherhood he's not as serious but I take that as a good thing considering one thing in particular he tried in the original FMA anime.I loved Brotherhood and I'm sure the changes were made so the versions of the anime wouldn't be looked upon as they were just simply re-done they decided to spice it up a bit..I honestly kind of liked some of the changes.
here's the 2 cents of someone that hasn't even seen it: The original FMA anime from what I heard was altered due to the fact the Canon Manga was ongoing. To add to this they would have had to make their own storyline from before the manga ended. From this I would assume that they altered the characters after they diverted from the manga storyline.
FMAB from what I've heard is meant to be the manga animated without needing to add content like the original FMA anime had to. Therefore the characters progressed in FMAB the way the mangaka wanted to.
I would also guess for Mustang's case that while the mangaka had an idea of what he would be like throughout, the anime companies didn't(since the mangaka could plan the story for chapters in advance and not let the anime company know)know what he would be like later via character development so they would have made there own and/or changed the character somewhat to begin with knowing that they wouldn't get the full story before the anime had to end.
PS: Since I know nothing on the contents of the FMA series I could be entirely wrong and only basing my ideas off how other anime's like Soul Eater had to have an alternate ending as well as using assumptions for how much the mangaka let the anime company know etc.