It's clearly the best version of Fullmetal Alchemist. There's room for debate with the two anime series. Both have clear and distinct strengths and both acquired massive, passionate international fandoms. There are reasonable arguments to be made for why either anime might be better than the other.
However as soon as you bring in the manga, there's no debate to be had. It outclasses both anime adaptations so unambiguously that trying to argue against it would be devil's advocacy. Its story is richer, deeper and more complete than the 2003 anime's and doesn't have the pacing problems of the 2011 one. It's better drawn. It's the definitive version.
I'll recap the story. Edward and Alphonse Elric are two small boys who lost their mother (wouldn't wish that on anyone) and are going to resurrect her from the dead with alchemy (hang on). This goes badly. They don't bring back a zombie mum, thank goodness, but they do lose a few body parts that will have to be replaced with metal prosthetics.
Well, I say "body parts"... Al lost his entire body. He's now a walking suit of armour, which Ed bonded to Al's soul in his own blood.
Fortunately, though, they might be able to get back their old bodies if they find a Philosopher's Stone! (They don't yet know that the magic behind those things is far worse than resurrecting your mother.) Our heroes have also joined the military, who recently invaded a neighbouring country and perpetrated genocide against its people. We're talking death camps. The triumphant mass-murderers now have a terrorist problem and it's far from clear that the terrorist doesn't have a point, despite being so consumed by hatred that he barely even seems human any more.
This is a rollicking adventure. It's got cool heroes, horrific villains and lots of entertainment. You could give this series to any small boy and they'd have a blast with it. They'd eat it up with a spoon. Me, I fell in love with pretty much the entire cast. Izumi Curtis is the most awesome housewife ever and way more cool (i.e. terrifying) than in either anime. Ed's a foul-mouthed brat with a hair-trigger temper who loves fighting dirty, but he's also hilarious and a true hero. Alex Armstrong is hysterical. I can't work out how I managed to become this fond of May Chang.
However it's also thematically rich. It's a 5000-page novel, effectively. Hiromu Arakawa incorporated many social issues into the work, for which her research included going to talk with refugees, war veterans and former yakuza. This is most striking in vol.15, which has no equivalent at all in the 2003 series, but isn't really done properly in the 2011 either. One of Arakawa's major themes is guilt and repentance. It's easy to say that soldiers who gunned down women and children are the bad guys... but what if you're one of those soldiers? You were wearing the uniform. You had to obey orders, didn't you? Arakawa talked to World War Two veterans and put the results in vol.15. Bloody hell. It's shattering. What they think today, how they feel... that's the volume that takes this series to another level. The soldiers are arguably the most important people in this series. They don't have superpowers. They don't have plot immunity and they can be gunned down in the street. It's perhaps more meaningful, I think, to see ordinary people like them putting their lives on the line to make the world better again. They're fighting for redemption.
Riza Hawkeye. Good grief, Riza Hawkeye. She got to me.
They need forgiveness and that's another theme. How do you forgive the unforgivable? This brings us to Scar, whose story is I think the clearest demonstration of how Arakawa's ideas are stronger than the 2003 series's enforced alternatives. Forgiveness vs. revenge. Look at how much Arakawa expresses through his eyes.
Another theme involves parents and children. The series is full of them, right from the beginning (the Elrics) to the last page of the last chapter and what's in that helmet. (Incidentally, do the Homunculus Father's past actions perhaps make more sense in a Buddhist context? Attaining enlightenment, expelling worldly desires, etc. His goals aren't very Buddhist, though.)
I'm tempted to suggest that the show's take on leadership might perhaps be linked with that. Roy Mustang, Lin Yao and Olivia Armstrong are almost obsessively loyal to their underlings, albeit cold-bloodedly in Olivia's case. One of Lin Yao's finest moments is the one where he scolds King Bradley for being a bad king (which is a bit like walking up to a Tyrannosaurus rex and poking it with a stick).
Then we have the moral ambiguities. This is a series where a gleefully unrepentant serial killer (Barry the Chopper) can be not just funny but cute... and it works. I think almost everyone in the cast has done something terrible. (Hohenheim!) That duality is pretty much the message of the island in vol.5.
The art's better. Anime needs thousands of pictures a minute, whereas manga can be built from all the most iconic moments. It found it fascinating. It's like a study in the handicaps of the moving image, compared with the inherent superiority of the original writer/artist. Well, here, anyway. The manga has quite a few images with far more power than the equivalent scenes managed in either anime. Mind you, there's something weird with Winry's eyes. She goes like a Disney character.
I love this series. It's mighty. It makes simple side characters feel integral to the story's message, e.g. the simple, paradoxical goodness of Mrs Bradley. There are so many bits I love, both big and little. Winry's angry face on vol.4 p96. "My scary thing is coming" on vol.7 p88. Greed on vol.8 p79. Mustang killing a helpless old man in the street and then being lauded by his men for keeping them alive. (And they're not wrong. That's in vol.15, obviously. I'd cite pretty much that entire volume, in fact.) Winry and Scar. Izumi, Izumi, Izumi. (Vol.20 p176 is just one moment that made me smile.) The soldiers' redemption in vol.22. Oh, and the silly chess pieces on vol.21 p48 made me laugh... well, mainly Olivia's.
Highly recommended. There's a reason it won awards and became an international mega-hit, you know.