Also, I found the manga to be much more sad. It's rare for me to cry with manga, but I cried a lot during Bokurano.
Now as for characters...First off is Daichi's story. I actually liked it better in the anime, since I felt they had a little more time to develop, so it was sadder in the end. But I was shocked and happy at the end of the manga, where they show that Daichi's father came back.
Mako/Nakama - I was shocked with how much her story was rushed in the anime. In the anime, her and Maki were the only stories that I cried for. I cried even more with the manga. I think the whole thing with Mako finding the schoolgirl during the attack added a lot. When she found her and said "I'm going to hit you" and punched her in the face, it was glorious. "Next time, help with the cleaning". Those words were so powerful. The uniforms she made also looked much better in the manga. Right before the battle where she screamed at Kako "Do you think I want to die?!", it's one of the few moments where a character outright screams about the situation. But unlike Kako, she didn't let her emotions get the best of her and kept fighting. When Yoko and Ushio are going back to everyone's family, the part with Mako's mom also made me cry. How she regretted letting Mako slip away like that, but then started crying in the uniform, when she learned that they nicknamed her "Nakama". Since the whole reason she was at the summer camp was to make friends. Mako is definitely my favorite character.
Kako/Chizuru - The anime and manga versions were really different, but I prefer the manga. I thought Chizuru's story comes across better. In the manga, Kako goes absolutely crazy and ends up being killed by Chizuru herself... And in Chizuru's story, the part where the teacher just left her there to get raped by those guys was painful. Even though I think it was wrong she trampled over the innocent people, I did support her in killing those people who raped her. If I was in her position, and I was going to die anyways, might as well go out, taking the people I despise with me.
Maki - I just love her story to death. I cried while reading it. In the manga it's clearly shown that her and Komo were childhood friends. The fact that she never got to see her baby brother in her Earth is heartbreaking. And even more heartbreaking is learning that her parents were searching for her, not knowing the truth. The visit with her parents at the end though was good closure.
Kirie - He is really developed in the manga, and his battle is also different. I loved the story with his cousin, and at the end where it shows she started eating again, another thing to make me cry. I loved how he tried to stab the teacher, although he didn't succeed. And him going out onto Zearth for the battle is risky but it really showed everyone that in the other cockpit are people just like them.
Komo - I was so shocked at how different her manga and anime versions are. Her anime version is like 1 episode, but her manga version is so much more developed and better. It was interesting to learn that Maki is her only friend and that she drowned the world out with books. I cried when she is reflecting on the world right before her fight, and how it took her so long to notice how beautiful the simple things are. And during her piano recital, the way she died right in front of her father was another thing to make me cry. Really, really sad. She was another one of my favorites.
Anko - Her manga version is also much better. I noticed that in the manga, she is more comical. But her story was simply amazing. She wanted to be an idol, and because of her message during the fight, she became the most famous girl in the world. She finally got what she wanted, but in a twisted way. Her fight was really interesting, and her legs got damaged :c. Another character that I cried for.
Kanji - I'm glad the manga didn't have any of that stupid stuff like the anime, how his mom is a professor and stuff. His fight was great. Seki sacrificed himself, but it was awesome how he went out singing the theme song to the anime that made him join the military in the first place. You also get a better sense of friendship in the manga with Ushiro and Kanji. Cried for him too, he was my favorite male character.
Kana - I never expected her to die in the manga. Only 10 years old... And the thing with Tanaka, where she pulls out the gun...I thought she was going to shoot the tentacles, but then I found out what she really was going to do. Big shock.
Yoko - She's an awesome character, but her ending was so jipped. Right about to sleep with Ushio, and gets killed. I wanted to see her pilot Zearth.
Ushiro - I really hated him at first, but by the end, I thought he was a really likable character. I thought he was going to survive till the end, but the author chose to take the route where everybody dies.
Dung Beetle - I can't fucking believe it, the author actually turned him into a likable guy at the end. I thought I would never like that jerk. Good job, author.
Anyways, as for the ending, I thought it was perfect. I didn't need to know WHY these battles where happening or anything like that, it's just the way the world works. I was expecting at least somebody to last until the end, but they all sacrificed themselves for the sake of their world. As for the other Dung Beetle at the end, I don't believe it was Ushio.
I'm going to be rating this 10/10, one of my favorite manga series. Saddest one I've read too. I need to make room in my favorites list on MAL to add this in.