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.
Alternate Character Interpretation - Are the humans who go nuts at the end being driven mad by Gaia, or did they just go stir crazy because Seno Miyagi declared that they would never return to Earth? Given the mystifying nature of the last episode, it's kind of hard to tell.
The Englishversions are considered by some to be better than the originals.
Designated Villain: The leaders of the space colonies are demonized for the grave crime of wanting to leave the bug-infested Earth (which had apparently decided to kill them all itself) behind for good.
Freud Was Right: The Blue's mouths look like female genitals (outer female genitals) and their weak spot is a tube that is destroyed by shooting or stabbing it, though, for a series like this, this actually works, as it shows humanity is more passionate about fighting for survival than it is loving and bonding with others.
Growing the Beard - For quite a few fans, the series improved sharply around episodes 10 and 11, when Yuji and Marlene escaped to space.
Marty Stu - Yuji Kaido throws morally self-righteous tantrums at everyone and barely ever suffers any consequence for it. Everyone goes on about how strong he is, yet most of what we see him doing is bouncing bullets uselessly off armour plating and emptying rounds wastefully into immobile corpses. At least three women fall for him, two of them pretty much instantly, all despite him being whiny, pathetic and generally ineffectual. He even tries to kill Marlene and never answers for it.
Memetic Mutation - The Blues looking like an "Angry Woman's Crotch." An [adult swim] card referenced this during the first airing of the series, and while people had brought up allusions to Vagina Dentata with the Blue previously, this really exploded.