These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Family-Unfriendly Aesop: Quite a few aesops that are typically shown as being negative as spun to give a positive twist. Such as envy, Fudou says that envy can either make someone attempt play dirty or use it as a huge motivator. Cue Sirius, using his envy for fuel along with the other two pilots, and spins his Aquarion around to make a monster of a storm and defeat the monster of the day.
Freud Was Right: One episode has Pierre show "addiction" to combining (yes, really). To cope, he takes a cup and a cup holder and repeatedly inserts the cup into the cup holder. He is also seen in that episode doing similar motions with a pen and its cap.
And to add to the double entendre, he spends his entire class staring at his female classmates (never the males). Granted, he is the Handsome Lech, but it is strongly suggested that this extreme is due to the addiction.
Funny Moments: Aside from all the unintentional humour from the merging, there's quite a lot to laugh at in this anime:
Gen Fudou, with all his wisdom, still has no idea how women work.
Sylvia getting increasingly jealous of Rena and Apollo in "Black Mirror."
Ho Yay: This show is purposely RIFE with it. Examples are: Baron and Apollo; Touma and Apollonius; Jun and Pierre; and Sirius and Apollo (mostly because Sirius is half of the reincarnation of Apollo's past life's soulmate; therefore, Sirius—along with Silvia—is Apollo's soulmate).
Moral Event Horizon: Touma killing Baron in Episode 13 and the army scientists killing Futaba then using his feathers to create superhuman killing machines.
With regards to the second one, it is treated as one, but considering that not only was it a viable way to end the war and save the human race from extinction, but also according to one of the overheard scientists, Glen volunteered for it, it might just be reasonable. When your enemy is indiscriminately taking humans for food, killing one of theirs to make weapons to survive doesn't really register on the Bad-o-Meter.
Also, it doesn't help that afterward Sirius spitefully stated that Futaba's life was worth far more than the people he killed, and we're apparently meant to agree with that.
Touma is really more of a Manipulative Bastard; he honestly thought of humans as we think of cattle. Plus Baron wouldn't have been killed had Apollo not grabbed the Schmuck BaitIdiot Ball and waited a few episodes.
One True Threesome: The ending with Toma, Apollonius, and part of Celion (i.e. Sirius) together forever inside Aquarion.
Tear Jerker: You will cry at least once during the final episode. Oh yes. You will.