Basque Gran is not quite as unsympathetic and 2-dimensional. He was brought in as a replacement for Armstrong after he basically turned tail and ran. He was also the one who found and secured the Supreme Cleric of Ishbal and gave him an audience with the furher to end the war, and he shot the superior officer who had little to no regard to the lives of his soldiers.
The atrocities were reduced/glossed over. No Armstrong letting two Ishbalan survivors escape , who then promptly get blown up by Kirabley.
No mention of rounding up Amestrian soldiers of Ishbalan descent, and the military using them, their own comrades, to create the first philosopher's stones
Nothing whatsoever about Winry's parents, which gave them a sympathetic human face before being killed, as they struggle while dealing with mounting wounded, no medicine, and patients who can't stand the sight of them
You lost any moments of Roy himself using his flame alchemy to kill Ishbalans, and you lose the moment near the end where he's basically ashamed of being considered a hero. And thus his realization and motivation to do the right thing, to rise to power to protect as many people as possible, is lost as well.
You lose the sight of Hawkeye watching her father die, which added to her trauma.
You lose the scene at the Ishbalan child's grave, and thus lose any sense of guilt on Hawkeye's part in helping create the Flame Alchemist through the secrets of flame alchemy tattooed on her back.
I could go on.