Outside of presentation, Aquarion's faces plenty of issues with its plotting and characters, in no small part because it felt like the series was trying too hard to appeal to various audiences. The show's plot seemed to be spinning its wheels for much of its run with "monster of the day" plots where Apollo and the teens faced off against different creations of the Shadow Angels while trying to figure out some vague hint dropped by their team captain, with the occasional hints dropped about Apollo's past life as a fellow Shadow Angel and a few of his teammates having their own connections to his past incarnation. However the revelations are nothing remarkable as the series doesn't really take much time to further flesh out the origins of the Shadow Angels and the Aquarion mecha created specifically to combat them. The show also could not seem to find a consistent mood to maintain in many of its earlier episodes where some come off serious, while others have a more comical bent. While the final 6-7 episodes do get somewhat more compelling with some shocking twists and developments that reveal more about the origins of some major characters, the show still devolves into a mess focused around mecha combinations and mysticism that the show had done a poor job of attempting to have complement Aquarion instead of being the anime's main attraction, which is laughably ridiculous with its pilots almost orgasming anytime the Aquarion's different formations combine together.
Not helping matters are the characters not having much to offer in terms of depth. All of the characters fill your typical anime character types in one form or another that include our lead Apollo as the rude and impulsive troublemaker, Silvia your short-fused noble girl with a brother complex, Sirius the attractive bishounen craving beauty and perfection, and team captain Fudou loaning enigmatic and vague hints that the teen pilots have to learn of. The Shadow Angels aren't much better off either as many of them are mostly two-dimensional baddies who look down upon humanity and see them as cattle for maintaining energy for their realm, with only main baddie Toma getting any sort of dimension for his character.
In spite of its impressive presentation, Aquarion is still a mess of an anime that loses focus over what sort of mood and plot direction it wishes to take its story, lacks any memorable characters due to how shallow they are, and trying too hard at attempting to please as wide a fanbase as possible. Overall, it's a rather forgettable entry in the mecha genre.
