Ishigami is much less likeable in the manga, his jokes being shown to be a front very early on, and being dropped altogether much earlier before his death than in the anime (which continues to shoehorn them in even after he dies via his holograms, the manga just gives us a Tear Jerker video for Katou's eyes only). The fact that he manipulates events using the foreknowledge the Machina Juda gives him makes him something of a Gendo Ikari with better PR.
How literal is Kouichi being when he promises to be a god or a demon if the Justice demands it? The Machina-induced mechanical face he has during the demon proclamation does NOT help.
In a way, Katou was training the Factors of Juda Corporation for the tribulations they would have to overcome under his command. He and Ishigami essentially incited a Lensman Arms Race that would leave humanity better prepared for the Human-Machina invasion, even though it was directly intended as such by Ishigami.
Broken Base: The anime adaptation, especially with how certain characters get treated and/or get derailed in the character development department. By far the biggest complaint was how the anime had severe cases of Mood Whiplash, swapping between serious drama and slapstick comedy every five minutes. The ending was also not well-received by fans.
Complete Monster: Riku Ousei is a sociopathicMad Bomber of the Katou Organization. While most other members have at least some redeeming qualities, Ousei delights in blowing people up from orbit with a Kill Sat just to make a point about his twisted concept of imagination (a bastardized take on his boss's own vision), and he is ready and willing to kill off a couple of innocent bystanders (a young man and his girlfriend who knew nothing of what was going on) just to taunt Koichi and drive him into a rage. After doing that, he was going to repeat the atrocity, this time targeting Koichi's Unlucky Childhood Friend Risako.
Case in point, Hisakata Katou looks like a pimp who talks like Lelouch, Sawatari goes about the place in a blue trenchcoat/suit thing with flames on the sleeves and pant legs, Demitri wouldn't look out of place in the aristocracy, and Masaki is dressed up like a goddamn cowboy!
In the manga, once the two organizations merge, they all accept the Juda black uniforms. Jack looks even more imposing in one of those.
Nightmare Fuel: The one time you see one of Izuna's nerve crack visions, involves the person affected seeing Linebarrel grow many times bigger than its usual size and transfrom into a massive deamon.
The manga gives us the story of Izuna's "defect", which is related to how he uses Nerve Crack.
Also from the manga, Miumiu, disgraced idol sitting atop a pile of fresh corpses.
The Machina-face of a Factor being affected by his or her Machina, rather than the usual way around. Very reminiscent of how the in-universe modern-tech androids look... But compounded by the glowing Factor eyes.
How many people get squished by the Armas and Machinas when they fight? How many Sawatari and Ousei squish on purpose on-screen?
Viewer Gender Confusion: 'sup, Satoru! His being male did nothing to stop the Anime adaptation from sticking him in a bikini during the Beach Episode. Also they refer to him as a she in the dub