It's a fascinating experiment. It was also enormously popular, even today for many people eclipsing the more faithful 2009 anime adaptation. I enjoyed it, although I think the ending's all over the place and it's marginally my least favourite of the three versions I've experienced.
Fullmetal Alchemist is, among other things:
(a) a manga by Hiromu Arakawa (2001-2010, 27 volumes)
(b) a light novel adaptation of the above (2003-2010, 8 volumes)
(c) an anime series that was... um, improvised from the manga's first two years. (2003-2004, 51 episodes, directed by Seiji Mizushima)
(d) an unrelated anime series that adapts the manga faithfully (2009-2010, 65 episodes, subtitle "Brotherhood")
I'm here to discuss the the Mizushima series, but I'll be comparing it with Brotherhood a lot. Which version is better? (The correct answer is "the manga".) Let's look again at the difference in quantity of the available source material. Only five collected volumes had been published when the Mizushima series started, although another three appeared during its run. In the end, the series used volumes 1-7. That's more than seven episodes a volume, although admittedly it feels as if about half of the Mizushima series was original material.
In contrast, Brotherhood galloped through at 2.4 episodes/volume. Its early episodes are particularly rushed. I prefer Brotherhood, but its pacing is clearly its biggest problem and Mizushima can spend far more time exploring its cast. One-off characters become regulars. We get more Sheska! I love Sheska. That on its own makes me happy. The show finds clever ways of showing character growth that in the manga got glossed over or happened offscreen. They're filling in the gaps and finding new angles on character points I hadn't previously thought about. What happened to Winry's parents is different, but just as strong. Similarly Maes Hughes is far more prominent here, which makes his story more powerful. Frankly, he's not that important in the manga and Brotherhood. It's not until the Ishval flashbacks that he acquires the weight he deserves, whereas in Mizushima he's a cornerstone of the story.
The homunculi have been humanised. Lust in particular gets character development far beyond her manga story role. I could imagine Lust's fans disliking Brotherhood for that reason alone. Mizushima also has some cool ideas about the origin and motivation of homunculi, which are fun to explore and work well within this different story.
Mizushima's Sloth is unique and great. She's a cool idea, she has cool powers and she's presenting our heroes with unique emotional challenges. Wrath is also a fascinating avenue to explore. My only niggle with those two is that their designs are too similar to existing homunculi, so Sloth ends up dressing like Lust and Wrath looks like Envy. In contrast, Arakawa's homunculi are all utterly unique.
Mizushima's homunculi are less dangerous, mind you, albeit every bit as evil. If you had a deathmatch between the two series, they'd get eaten alive. (I don't really mind that, but the manga's Wrath vs. the same man in Mizushima is... ahahahahaha, no.) In this series, the most badass homunculus is Envy! These homunculi are all basically people with a few superpowers, whereas Arakawa's homunculi are liable to be Lovecraftian elder abominations, the Incredible Hulk and/or dinosaurs made of screaming human souls. Similarly Mizushima's homunculi aren't really working to much of a plan, except "make philosopher's stones" and "be evil". There's a villain with a goal, but nothing that measures up to the manga's Father and the terrifying scale of his operations. The manga has a ton of plot, which Brotherhood struggles to cover in 65 episodes. Mizushima has different pacing problems. The first quarter feels a bit aimless and the series almost never feels rushed, but then the last few episodes are a mess of "what the hell?" ideas, new story elements out of nowhere and characters shuttling between worlds as if there's a bus service.
There's an animated movie sequel, but I don't think that's an excuse. Apart from anything else, it didn't hit cinemas until 2005.
For the most part, Tomoko enjoyed this series. She finds its homunculi more emotionally engaging and she liked what the series (hastily) does with Selim. However the last few episodes made her go "eh?" and she basically thinks the show lost it at the end.
That said, though, it's still Fullmetal Alchemist. Even a lightweight version of Arakawa's storyline is still meaty, with genocide, rape, innocents getting gunned down by the military and more. At its darkest, it arguably feels more doom-laden than the original. It's still a family friendly show, mind you. No nudity, onscreen violence occasionally a little bit gentler than I'd been expecting, etc. Natsuki watched some of the episodes with us and he thought it was less exciting and fun than Brotherhood. (He's two. You can judge his opinion by how much attention he's paying to the screen.) In any incarnation, this show is meaty, thematically dense and saying vicious things about what happens when we go to war.
It's also almost without filler. This used to be surprising from a 26-episode show, let alone a 51-episode one. The storyline's always moving forwards and I think only someone comparing it with the manga could find themselves asking for more.
The story's about different things, obviously. All versions of Fullmetal Alchemist have a lot to say, but the emphases differ. This series is less about action, I think, partly because it's talkier and partly because occasionally it's not very good at action (e.g. ep.5). It's stronger in its portrayal of purely human evil, with the military running everything for their own convenience. It wasn't homunculi making them do it. We can be evil all by ourselves. The army politics is stronger here, with the generals' self-interest being more sinister. The series also wants to dissect the principle of equivalent exchange that underpins this universe's alchemy. I don't think it really succeeds there, to be honest, but it's making a wholehearted attempt.
A few characters are slightly off-model, although it's understandable. Hohenheim and Kimblee didn't feel quite right to me. I reckon they made Hohenheim younger deliberately, but with Kimblee I suspect it's simply that he'd only had a cameo in the manga, so the anime's character designer hadn't had much to go on.
I dislike Paninya in different ways in the two versions. In the manga, she's cool and likeable, but a moral vacuum (although she'll grow out of that). Here, her characterisation has had all the rough edges sanded away and is inoffensively anonymous, to the point of not really fitting into her own episode any more.
The first quarter of the show doesn't feel particularly urgent. There doesn't really seem to be a storyline as Ed and Al drift from incident to incident, although in fairness that's what the manga's very early chapters do too. The anime even adds a filler episode or two. (They're weaker, I think.) However the show takes a big right turn around ep.15. That's the first major change. That woke us up. After that, we knew we had no way of knowing what was going to happen in this universe, which becomes twice as true in the second half when the show goes off in original directions.
Almost everything from vol.1-7 of the manga has been included, but sometimes shuffled around or reworked. Vol.8 is where we lose sight of the manga. None of the Xing characters (Lin Yao, Fu, Lan Fan and May Chang) are here, for instance.
Before I started watching, I'd been assuming that this series would be faithful until they ran out of manga. Only then would they diverge, surely. Boy, was I wrong. Plenty of things are at their best in this series, though, which is interesting if only for its differences. It has the strongest version of Maes Hughes's story. Ed and Al on the island are done better. The biggest surprise at the finale makes me laugh. I still prefer the manga, but this version's worth your time too. It's just that the manga has more story, a more satisfying ending (I think) and just as much richness, characterisation and thematic depth. Mizushima's version of Mustang's soldiers, for instance, can't compare with what the manga's later chapters do with them. The manga's a denser experience, not to mention bigger, more epic and starring plenty of characters who don't appear here at all.
Nonetheless Mizushima is still a hugely successful series that reinvented its source material so thoroughly that it can surprise you with revelations that you theoretically knew already. It's strong, funny and wholehearted. It's bringing alive a big cast. A generation of anime fans fell in love with this show and it's easy to see why.