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.
Freud Was Right: The way the girls (Dita and Jura more than Meia) fight over who gets to combine with Hibiki, not to mention Barnette's jealousy of Jura's intense desire to combine with Hibiki and the fact that a Vanguard can only combine with a Dread, not another Vanguard...yes, the Combining Mecha are totally a metaphor for sex.
The Tarak ship and the pirate ship combining, with Bart as its pilot Buck-nekkid and all) represents reproduction.
To analyze that metaphor further, the Nirvana's development of what amounts to a Wave-Motion Gun and the uncooperativeness of the Paxis at the time are an obvious analogue for Puberty, and the actual firing of said gun could be one for ejaculation.
At least early on, whenever Hibiki and the girls were done, the boy was absolutely exhausted for no real reason, especially if he combined multiple times in a battle.
In that case, the Super Vandread would be an analogue to a... fivesome? Hibiki, Dita, Meia, Jura and not to forget Pyoro...
Maybe a convoluted summary of their final relationships, or that they are one big happy family?
The first time Hibiki and Meia combined, when we first saw them after the last Harvester was destroyed, they both collapsed in their seats exhausted, taking in deep, panting breaths. I think they were sweating too.
Seriously? How has no-one mentioned Dita's highly... suggestive bouncy-ness after the second use of Vandread Dita??? XD
Fridge Brilliance: At first glance, the fact that EVERY female on the ship (who is neither absurdly old nor young) is VERY well endowed seems to be plain ol' fanservice. However, given the fact that the Pirate's home planet was created so that reproductive organs could be harvested for use on Earth, it makes perfect sense that Mejale women would be better equipped than normal. This is made more apparent by Misty's (a non-Mejalian) being of relatively normal build as compared to Dita, who is the same age yet FAR more developed.
Hibiki is similar, being rather scrawny compared to every other man he's known. Then it turns out he, unlike the others, he was not grown in a factory. Hibiki hasn't gone through gene therapy at all and thus lacks some manly advantages.
Fridge Horror: We don't actually see the harvesting process occur on-screen, but it's implied that victims often aren't killed before being getting torn to pieces.
Game Breaker: Super Vandread, so much so that it wasn't used outside of the finale after its first appearance because it would win all the fights in five minutes. And even then, the only thing that can prove a challenge to it is the single most powerful ship in the Harvest Fleet.
HSQ: Bart unlocking the Nirvana's Beam Spam and later, Super Vandread's debut.
Les Yay: It is mainly between Barnette and Jura, justified in that they were both from a lesbian-based world setting. In Second Stage, it happens briefly between Misty and Meia.
Moral Event Horizon: The humans still on Earth cross it by creating the aliens that the Nirvana's crew regularly fight against in order to harvest the organs of their spacefaring brothers and sisters for the sake of self preservation.
An interesting note about Pyoro. Before he became a scrappy, he was an emotionless automaton with hardly any emotion whatsoever. However, he's still a candidate for scrappydom by being intensely irritating Plucky Comic Relief.
Villain Decay: Averted with the second Harvester mothership, which learned from earlier battles. It takes a Heroic Sacrifice by Gascogne to stop it. Played straight with the three motherships in the Grand Finale, where they are destroyed rather easily. Of course, this is probably due to the fact that they were being ganged-up on by the fleets of three planets, one space station, three cool ships and a hijacked Harvester mothership, courtesy of Gascogne, due to not being Not Quite Dead. Not to mention, they were in the presence of theBig Bad. The Evil Knockoff of the Nirvana also suffered from this, having TWO of them easily defeated by the Vandread Dita and the allied Redshirt Army, despite being nigh-invincible in its first appearance.