Some other things I think were very important in the Ishval arc that weren’t mentioned in Brotherhood:
Basque Gran’s minor coup was not simply over reckless orders. The Ishvalan religious leader, Logue Lowe (who had previously been in hiding in the wilderness), along with an escort group, had approached them asking to meet with Fuhrer Bradley. Logue Lowe intended to offer up his own life in exchange for stopping the war.
Hughes, Gran, and all the others seemed very humbled and a little sad, and respectfully granted his wish, bringing him to see Brigadier General Fessler. Fessler refused incredibly disrespectfully, and that was the final straw for his men.
Gran: Logue Lowe, supreme cleric of the Ishval region. I brought him here because he requests an audience with the president.
Fessler: You fool! I don’t care if it’s Ishvala himself! My orders are to kill them all! …Take these Ishvalan dogs out back and shoot them!
Gran: Brigadier General Fessler. An interesting statistic: Did you know that half of all officer deaths on the battlefield are attributed to assassination by subordinates?
Hughes: It was a stray bullet.
Unnamed soldier: Yup. That’s what I saw.
Gran: Now that General Fessler is dead, I have no choice but to assume command.
Soldiers: Yes, that’s the only course of action. Please take command, Colonel Gran.
Gran: Captain Hughes, take Lowe to the president! Second Lieutenant Belmot, take the injured to the back immediately!
Lowe: Should I… give you my thanks?
Gran: I need no thanks from you. I just pray that your negotiations with the president go well.
(From the Viz translations, edited slightly for conciseness + name corrections)
This was important because it shows us that even Basque Gran, a character generally known for his cold demeanor and ruthless fighting tactics, has some moral limits and wanted to end the war.
After they took Logue Lowe to see him, Bradley very rudely shot down his attempts at negotiation, saying that his life was worth no more than anyone else’s. He ordered Lowe and his escorts to be killed, while also going on a tangent about how there’s no such thing as god and that religion is stupid, because if it’s real than why didn’t Ishvala strike him down yet?
It also showed a lot of Scar and his brother, and Sarah and Yuriy Rockbell. In the anime it’s only mentioned that the Rockbells treated Ishvalan patients, but in the manga we get to see that they were truly risking their lives. Not only that, but they were constantly understaffed and undersupplied, with so many injured. At one point, several Ishvalan children pitched in to help them, since they literally could not do all the work on their own. Also, an ally who was bringing them supplies heard news that the military planned on purging Ishvalan sympathizers, and begged the Rockbells to flee to safety, saying that they had already done so much. They refused, because there were still more people that needed their help.
It was also revealed that Aerugo, who had long been at war on and off with Amestris, had been supplying the Ishvalans with weapons and other supplies in order to wear down Amestris. However, when Ishvalan refugees (including Scar’s master) attempted to flee into Aerugo, the Aerugonian government shut them out. They were using them, nothing more.
Knox was initially a surgeon, but was given orders to participate in a project gathering information on the effects of various types of bodily harm, using Ishvalans as test subjects. He asked Dr. Marcoh, “I’m a doctor, so why am I killing people?” On the opposite page, we have Riza asking, “Why is alchemy being used to kill when it’s supposed to help people?”
Kimblee was given a Philosopher’s Stone to test out in secret. After he gave his report and was ordered to return the Stone, he killed all of the men who knew about the Stone so he could keep it for himself. That’s why he had it in prison way at the beginning of the series; aside from Envy, nobody knew he had it.
The men in Roy’s squad- Charlie, Fabio, Richard, Alexandre, Dino, Albert, Roger, and Damiano- are the same men who later aided him in the coup d’etat on the Promised Day. They were so grateful and loyal to him for all he did to protect his subordinates in Ishval that they were willing, years later, to help him even though that meant going against the military. In the anime, since that entire scene was cut, nobody knows who the hell these random guys who showed up to help are or why they seem so chummy with Roy and the gang.