Why was Shinn the only member of Compass who wasn't bowing towards Aura? He just forgot to. Apparently disrespecting higher authority is just that second nature to him.
While everybody is talking about serious politics and world affairs at the Foundation's party, Shinn is enjoying the buffet and seen eating a massive plate of food. After Luna and Agnes talk, Shinn is seen with two smaller, but still stacked plates filled with nothing but desserts, with the implication being that Shinn went for multiple rounds of food. It's rather surreal to see that the once remarkably angsty kid from Destiny is quite the Big Eater.
The entire existence of the Z'Gok. Unlike most Cosmic Era units imported from the first show, the Z'Gok does not have a sub-name like how we have the ZAKU Warrior, or the DOM Trooper, it's just the Z'Gok, which makes it funny. There's also the fact that Athrun is amazingly adept in the Z'Gok fighting style, able to hold off Shura single-handedly by basically engaging him in a fistfight while the latter has a lot of beam sabers until Shura had to retreat, and the fact that somehow the engineers who designed the Z'Gok managed to cram the Infinite Justice in the thing.
The Foundation betraying COMPASS was horrifying, and not funny. However, what is funny is that Shinn unintentionally gropes Hilda's breasts while watching the nukes go off in sheer horror, and the latter merely blushes.
When Kira and Athrun come to blows over the events surrounding the Foundation's surprise attack on COMPASS, Shinn tries to play peacemaker between the two, only to get accidentally punched aside by the two childhood friends, both of whom didn’t even seem to register that Shinn tried to intervene. Even after being knocked to the ground, Shinn was up and ready to step in again and make it a free for all, but Hilda stops him. What makes the fight even funnier is that Athrun (the one with the most military training of the trio) is completely in control of the scuffle. Kira doesn't land a hit once.
When the Archangel crew enact their plan to hijack the Millennium, it's implied that Alexei Konoe and Albert Heinlein knew that the hijackers were their MIA comrades, as Konoe is slouching, bored and waiting for the hijacking to be over with, while as soon as Murrue and Kira break into the bridge, Albert greets Kira casually.
Meanwhile, Shinn, while hijacking the Millennium, wearing a helmet, tells Lunamaria not to move.... only for Luna to disarm him. Shinn panics and right before Luna puts a bullet in Shinn's head, Shinn takes off the mask, yelling in sheer terror, "It's me! It's just me!". Luna was initially happy that Shinn was alive, much to Shinn's confusion, but then she turns angry that Shinn tried to take her hostage and slaps him over and over, while Hilda walks in the scene with a face that basically says, "What the heck is going on?".
The novel makes this scene funnier as this was Shinn's idea to surprise Lunamaria, except the surprise backfired so horribly that Shinn had a self-realization on how incredibly stupid the idea was in hindsight.
After Murrue accepts the captain's chair and Alexei gracefully demotes himself to XO, Arthur is wondering what's going to happen with the new command structure... And then he realizes he got demoted, as he was the XO for Alexei.
During this scene, Shura has a face that screams "Oh, Crap!", as Orphee looks at Shura, questioning how the hell did Kira survive not just Shura's attempts to kill him, but yet another nuclear explosion that was meant to explicitly finish COMPASS off.
The Fridge Hilarity, if one thinks about it, in that the Foundation is Crazy-Prepared enough to making their mobile suits specifically to fight anything Kira pilots, predicts and calls call out Orb on pulling the "Bomb the ship with artillery but miss them" trick yet again, even calling it cliché in the novel... yet fail to somehow take into account Kira Yamato's inexplicable survivability odds surviving nuclear explosions.
Shura tries to read Athrun's mind... only to get a glimpse of a naked Cagalli with a very amorous expression, causing him to scream in shock. The fact that this is what protects Athrun from Shura’s psychic assault, and that Shura wasn’t at least somewhat titillated by the vision, instead straight up horrified, is just priceless. Shura venerated Athrun as a Worthy Opponent but Athrun's constant trolling of him throughout the movie gradually makes Shura lose respect for him, culminating in Athrun trolling his mind reading which ends up being the final straw. Athrun's said trolling makes one wonder if he is quite the Covert Pervert, because he has quite the proud smirk afterwards, or if he was simply relying on Refuge in Audacity to throw Shura off his game, in which case it worked too well. And it begs the question if this was just Athrun's fabricated imagination, or a memory.
Shura: You shameless cur! The battlefield is a sacred place, yet how could you think of such a shameless fantasy!?
Even better, Cagalli was listening in on Shura and Athrun's conversation (even from several hundreds of kilometers away!), and she realizes instantly that Athrun thought of her naked. She's not happy about it.
Cagalli: [listening into the conversation and thinking of Shura's words] A shameless fantasy? [blushes angrily after realizing that Athrun thought of her naked] Athrun!
Made doubly hilarious when Athrun ends the fight via a beam blade on his antenna. He literally beat him with the power of horny!
Mixed with Awesome, but Mu casually tanks the Requiem with the Akatsuki like nobody's business. Rule of Three indeed. He even lampshades it.
Mu: It's tiring being the man who makes the impossible possible.
Shinn addresses Mu as "old man". The latter's response?
Mu: I'm not an old man!
Considering by now Shinn has likely made amends with Mu's time as Neo Roanoke, one can imagine if this his way of teasing him the older pilot.
Shura duels the Strike Freedom Type II while defending Artemis, only for him to realize that his fighting style is different. Cue the reveal that Kira was busy rescuing Lacus and that Athrun was actually piloting the Strike Freedom and trolling Shura at the same time. Athrun then proceeds to taunt him just to piss Shura off.
Shura: You-! Athrun Zala, I take it?
Athrun: [Makes a really smug smile] I thought you could read minds? Not very useful, huh?
Shura: [Yelling with anger] I'll kill you!
Kira gets in a particularly funny line in on Orphee that throws the latter off in the final fight.
Orphee: In terms of specs, my machine is better than yours. What chances do you have?
Kira: I have a weapon, one that has always helped me until now!
Orphee: And what would that be?
Kira: [Does a full burst attack and activates SEED Mode] Lacus' love!
During Lacus' rescue from the Foundation, a literal army of Haros bounce through the airducts of Artemis, gassing everyone inside the fortress. It's as silly and as awesome as it sounds. Even funnier is that once they release the gas, we get a quick cut to the navy one with the Turn A mustache...and it speaks Gym Ghingham's "GEKKOUCHOU DE ARU!", complete with Takehito Koyasu's voice.
During the final battle, when the Black Knights try to misdirect Shinn's thoughts the way they did Kira's earlier in the movie, but fail. "Doesn't this guy think?!"
When Stella’s spirit protects Shinn’s psyche from the Black Knights, she morphs into an abominable distortion of herself that almost as comical as it is horrifying. The Black Knights' collective reaction to this also warrants a laugh.
While it is mostly heartwarming, the fact that the very last scene in the movie, and at the time of the movie's release, in of all of Cosmic Era, is Kira and Lacus naked, on a beach, and making out. There's also the implication that Kira and Lacus were so sexually pent-up that, immediately after killing Orphee and Ingrid, The Chancellor and Secretary of State of the Foundation, instead of dealing with the politics of killing the leaders of a nation, they ditch the battlefield, parked the Mighty Strike Freedom at some random beach on Earth (The Mighty Strike Freedom still has its battle damage on the railgun and the chest is scarred), and they decided, for some reason, to have Their First Time right then and there.
To further add to the funny, but also heartwarming, considering that the last time Kira had any was 4 years ago, when being sexually manipulated by Flay, one wonders if he also wanted to do it immediately after the battle because he was pent up.
Meta-wise, the casting of Yukari Tamura as Aura Maha Khyber. For the longest time, Nanoha has been compared to the Gundam franchise, infamous for firepower on par with the most broken late game machines, taking the original Gundam's nickname of the "White Devil". Here, in her first actual major Gundam role? A COMPLETE opposite to Nanoha in every way. A tyrannical Smug Snake eugenicist whose child-like appearance is due to accidentally deaging herself too much, and a total non-combatant who can't even Face Death with Dignity when Millennium rams right into her ship. Hell, while she does slaughter millions in Eurasia with Requiem, as mentioned above, the one time she specifically targets someone using a giant Wave-Motion Gun, she misses.
The light novel with Athrun and Cagali, Escape for Two has some funny moments:
Athrun reading a menu and being confused about the food, like monjayaki and modanyaki (A savory Japanese pancake, and a savory pancake on top of noodles respectively.) For the latter, he wonders why it's called a "modern yaki" (Modan being the katakana for modern), even thinking the latter is overkill on the carbs. He also sees a dish called the Haumea Lava Grill, and questions whether it's okay to eat that because Haumea is part of Orb's Pantheon, and he thinks that eating a god would be considered blasphemy.
Athrun and Cagalli talk about food, and it turns out that Athrun is not a foodie whatsover, while Cagalli is, and if anything Athrun is quite the picky eater, initially hesitant to try the monjayaki, until Cagalli makes him try it and he reluctantly admits it's delicious. He tells Cagalli that Waltfeld would be a better foodie and would enjoy this place, but Cagalli refuses outright because "Any man who drenches kebabs in yogurt sauce has questionable taste".
Turns out the restaurant Cagalli likes is a place to protect her from potential threats, and Cagalli is not amused that she's getting protected. Thus she gets Athrun to "kidnap" her and Athrun nearly starts an international incident because Cagalli wants to get away from her security.
In desperation, the Orb Security forces call Murrue and Mu for help, only for them to realize that since the kidnapper was Athrun, Cagalli is just running away from her guards again. The two laugh it off.
While not stated, it's somewhat implied that the novel took place during the first third of the movie as Athrun was spying on the Foundation and around this time, the last Blue Cosmos headquarters was found between Eurasia and the Foundation homeland, which is why COMPASS went to the Foundation capitol. Basically, while Kira and the others were at the ball, Athrun went on a food date with Cagalli, nearly caused an international incident by "kidnapping her", and he still had to take the Z'Gok to where Kira and the others were right when the Foundation betrays COMPASS. Basically, it's implied that Athrun didn't show up until the last second because he was dealing with a date, and if Athrun was one second late, Kira would have been killed.
