When the show manages to slip in a funny moment, it stands out all the more. An example? Well, the episode where Hiroto barricades himself into a classroom, and Kiyomi recalls a similar occasion... where Maya's sister Yumiko climbed up the lighthouse and announced to the whole island that she would become an idol singer!
Shortly thereafter Kenji, in his position as student council president, tries to help lure Hiroto out. He makes a huge wind about the job too only to find out that absolutely no one knew he was student council president. Everyone thought it was Soushi. Even his mom.
Mamoru's parents are actually backwards complimenting him, earning a "What the hell" from Yoko.
When Kazuki is asked about his reason, his reply is that he has no special reason (except that he doesn't want Maya to fight), which earned a facepalm from his father.
Mizoguchi even joins in and say he accidentally altered the data when he was looking for Maya's measurements, which earned him a "Shut Up" from the committee (And a continued facepalm from Fumihiko). And the fact that he was asked to testify from the audience seat because it was too troublesome for him to come around to the defendant's stand. Oh, and he's going to read that out loud if he's not told to shut up.
When Tsubaki takes the stand, everyone's reaction was "This is like bringing God to the court!"
The sento sequence is a large one, but it really takes the cake when the girls harassing Canon on the opposite side, the male cast are certainly enjoying it......Except Kazuki and Soushi, who just exchange a few words in deadpan.
Kazuki: What is it?
Kazuki putting on Mamoru's helmet also counts. Especially considering Soushi's look of complete and utter disgust.
Soushi: I refuse to cross with you looking like this.
Combines with Crowning Moment of Awesome. Even this series has one, in the finale after Kazuki and the Mark Sein had been absorbed into the Festum world and it looks like he might get out of it, the Mark Nicht with Idun appears in the real world proclaiming "I'm still here!". Only to be covered in crystals and assimilated by the Sein and Kazuki. Those who hated Idun this comes off as both awesome and funny.
Soushi cooking with a thermometer and a chronometer. Soushi in an apron doing any household chore, really. Look how proud and confident he is. Of course this promts an old joke to raise its head.
Kazuki: You're really awkward, aren't you?
Billy asks Maya if she has a boyfriend and Akira pops up immediately with a SHE DOESN'T!!
Maya finds out that she has a half-brother who is a member of the Human Army, and confides to Canon about it. Due to not supplying the context, Canon misunderstands and thinks Chizuru and Fumihiko got busy.
When explaining each characteristics of the three new pilots, at the end of each pilot's description, Sakura gives a note in Layman terms, by comparing them to Kazuki, except Sui, which was compared to Soushi.
When Canon tries to explain the characteristics of the Fafners (Which is repeated once in the original series, OVA and movie), Sui keeps cutting her and completing her sentence. He is ultimately stopped by the combine elbowing of Leo and Mimika.
Just the fact that he now has to deal with Goubain Generation 3. You almost feel sorry for the guy, straight-laced and stoic as he is, having to deal with that shit again.
The character duet Taiyou to Tsuki that was released with the second DVD/BD of Exodus is so upbeat and happy sounding that it took almost everyone by surprise. And then you read the lyrics and it's hard not to laugh. Are we sure this song is related to Fafner?
Reactions from Kohei Kiyasu (Soushi's VA) in various interviews about this song are downright funny.
Kazuki trying to cut his own hair with scissors he obviously filched from the medical tent. When it doesn't work Soushi says he'll "show him what a real haircut is" and proceeds to cut Kazuki's hair for him. With a ruler, because it has to be perfect.
Soushi: A difference of five millimeters...I'll have to correct it.
Kazuki: Jeez, you're so awkward.
Kazuki's affectionate smile makes it into a CMOH at the same time. As does the tone he delivers the line in. In the original show he was just baffled every time Soushi displayed his awkwardness but now Kazuki just seems to think "yep, there we go. That's the Soushi I know and love" and it's heartmelting.
Kurusu spends half of the Episode 22 naked, even during a long conversation with Chizuru, Yumiko, Miwa and Emily, before asking for clothes.
Kurusu vs Chocolat.
Kurusu: I don't like you much. Because you fought the last core, I guess. Why don't you go somewhere else?
Kurusu jumps behind Orihime in fright as Chocolat growls at him.
Kurusu: No! Help!
Orihime: Why are you scared of a dog?
Kurusu: Why aren't you?!
Even the serious, action-backed penultimate episode could help but put a small moment, in which an 18-19 year old girl says something she probably shouldn't say to a 14-15 year old boy.