S1E12: Two characters are seen eating an animal they trapped and killed.

In more ways than one. Combined with does a kid die"

several animal-based chimera are killed, a couple human-based chimera are murdered.

If you mean by illegal experiments, yes, very much.

In the tunnel created by Sloth at Fort Briggs, horses are killed.

There are ants during the flashback about Ed & Al's training. Later in that scene, someone eats some ants out of strong hunger.

Does a snake chimera (a fusion between a human and a snake) count? If so, yes.

one of the characters, Jean Havoc, is a smoker

a few characters drink alcohol, and one is implied to abuse alcohol (has at least one alcohol binge but doesn't drink on screen)

At some point there is a shaving razor shown resting on a sink, but not in use.

One character loses limbs in alchemic accidents, another cuts off their own arm after it is injured badly in a fight. These are both graphic amputations. Several other characters are amputees and also have automail, or artificial limbs, and are sometimes shown without their automail.

Yes, at least twice on screen, maybe more, characters are rather graphically set on fire multiple times until their regenerative abilities stop working and they eventually die. Lots of screaming, so it obviously still hurts even though they aren't human. Also, mentioned quiet a few times, and a minor character is believed to have been burned alive, but this was faked. One character is literally called the Flame Alchemist, and it's mentioned, and shown, that he used his abilities to help in a military sponsored genocide. He is haunted by this and did not enjoy doing it, so... ? He's not a totally awful person?

Yes, particularly if the head doesn’t belong to a human being.

no actual seizures, but a few scenes of people convulsing that can be seen as similar to a seizure

A battle between Envy (who can regenerate) and Mustang (who can control fire) involves Mustang repeatedly burning Envy's eyes out as a form of torture, shown multiple times as Mustang specifically calls attention to how painful it must be. Definite yes on this one.

And loses limbs, or gets impaled, or has their entire body disappear for a while.

The series began with the main characters' mom dying and them trying to bring her back to life and failing; it is pretty disturbing.

This one's infamous. Early in the series, a young girl is turned into a chimera by her father, and is later killed by Scar.

Both shower/bath scenes are of minors, though nothing "important" is shown.

many characters are constantly under surveillance by one or more characters/organizations at different points of the series, as a looming threat

During Episode 42, when Hohenheim enters the tunnel, there is a brief period of silence after he notices that an enemy is already present, before a sudden screeching noise as Pride (made entirely of shadows with teeth and eyes grotesquely mashed together) speeds out of the darkness to attack him. It can be quite frightening without warning.

It depends on what you mean by ghost. The souls of dead people are shown and in most cases obviously in pain and/or screaming. There are no "ghosts" per say but the state of these souls is important to the plot

Greed possesses Ling's body (though he willingly agrees to it)

one character has a spit-based attack

In one episode, Ed gets sick and vomits twice, you hear the sounds but don't really see the vomit itself

There certainly is electricity, as various alchemical abilities appear in zaps of energy, but what it is meant to do is the opposite of therapy.

Characters frequently get injured, and wind up spending a surprisingly large amount of time in hospitals

About halfway through S2E13, Reunion, there's a brief but explicit shot of a character being injected with something that is obviously extremely harmful.

Barry the Chopper convinces Al that his memories were faked and that he is a made-up person in episode 8. The consequences of this are explored in the next episode.

This is much of what drives the Elric brothers to get their bodies back for the entire anime, after one losing an arm and leg, and the other losing his whole body — that his soul was attached to a suit of armor. Comparing to real life, clearly those who are severely injured or amputated have trouble accepting their bodies.

No. One character is literally a suit of armor and physically cannot eat for most of the show. Another doesn't like milk, but no evidence of eating disorders. Lots of mentions of armor character wanting to try foods when he gets his body back.

Ed definitely seems to struggle with some degree of PTSD, and is shown to experience nightmares and flashbacks to previous traumatic events, usually accompanied by moments of panic. There are other examples, but this is the most prominent

Various scenes of characters in cramped spaces, including climbing through vents and going inside Alphonse’s armor.

SPOILERS: Envy technically dies by suicide when he rips out his philosopher’s stone.

There are a few instances where characters harm themselves, but it's not done out of usual circumstances or depression: Examples such as a character tearing open her chest to reveal her Philosopher's Stone that allows her to regenerate, and shortly afterwards, Mustang uses Flame Alchemy to burn his own wound to cauterize it, while also carving a magic symbol into his hand in order to cast said Alchemy to fight back.

Episode 11, "Miracle at Rush Valley". Nothing graphic or body-horror-like, but the situation is depicted as extremely stressful due to suboptimal circumstances as the mother is giving birth. Everyone involved is fine in the end.

Can't remember if it was specifically a miscarriage or stillborn, but the brothers' teacher attempted to bring her baby to life with alchemy.

No, all pregnant women survive.

Not in Brotherhood. Don't confuse this with the 03 version, where it is implied that a female character is.

There is a mildly sexualized character, but it is not done so in a creepy fanservice way.

Ed and his love interest, Winry, are childhood friends. However, they never considered each other 'family'.

there are no explicitly trans characters in the series, but a side character that can be seen as a transmisogynistic or homophobic stereotype.

darius is gay and he survives--- http://fma.wikia.com/wiki/Darius (scroll down to trivia section)

No hate-speech from the author directed toward a minority group, but plot-wise, the leader of the nation decrees mass genocide of a certain group of people.

no, but there are a couple characters that can be seen as racist caricatures of black people

the character gluttony is constantly mocked for being fat. There are also many jokes about height and muscular body types.

recurring themes of amputees feeling "not whole" but overall positive towards disabled characters (which there are many of)

(spoilers) One of the major villains, the leader of the country, has a visual and thematic resemblance to Hitler. Even his title is the same.

The end is both happy at times and bittersweet. But I think it's a happy ending.

One character early on kills his wife and functionally tortures his daughter.

During the Alphonse fight in Ep. 52 "Combined Strength."

Not a nuclear explosion, but one character's alchemy is literally blowing things up. If you're uncomfortable with it, avoid watching anytime Kimblee is mentioned, cause he really enjoys what he does, and it's sickening.

To name just a few: Edward (15), Ling (15), Alphonse (14), and Mei (10) all experience serious/life-threatening injuries at various points in the series. Nina (5) is turned into a chimera by her father. Selim (though a few hundred-year-old homunculus, is presented to be around 9-10) gets brutally beaten at the end of the series.

Episode 08 "The Fifth Laboratory". In a brief phantasmagoric when a criminal retells his past, there is indeed a hanging shown.

At one point, it appears a (villainous) character has fallen into a body of water and died, but the character survives the fall.

The Silver Alchemist drowns after being attacked by Scar

Many of the charcters are military officers and use guns

Mostly blood

iirc I don't think anyone gets injured or killed

A villian get stabbed and then burried alive in concrete