In the anime Super Dimension Fortress Macross, Zentradi are a race of giant alien warriors, genetically identical to humans and capable of being reduced to human size. They function as proxy forces for the unseen and extinct “Protoculture” race; there are no civilians and the sexes work separately for the same military goals.
They attack Earth, but some find that exposure to Earth’s culture, (especially to the music / persona of pop star Lynn Minmay), awakens repressed desires and causes them to question their system. A portion of Zentradi ally with humanity to gain these freedoms, and to save themselves from the authorities that now consider them contaminated. Following these events are a franchise of Macross series, in which internal unrest from allied Zentradi is a recurring plot point, due to a tension between the Zentradi past and their future.
Some fans have looked at these events and decided that humanity allying with the Zentradi was meant to be a fundamentally self-destructive move. “Self-destruction” can be defined in two ways.
1. The rebellions of allied Zentradi become intense and enough that the alliance becomes philosophically invalid.
2. Zentradi were emasculated by their choice of human contact, sacrificing their power and gaining nothing in return; other factions of Zentradi are even killed.
Either way, it suggests that the ultimate goal of the Macross plot was to undermine the alliance it set up, a cynical universe in which allies might destroy each other.
Yet the case for the this is not strong enough. The internal conflicts never lead to the destruction of the entire alliance, and there are positive Zentradi characters to counter them, not to mention the idealistic tone of the entire franchise.
Viewers confuse the presence of conflict with the rejection of previous ideals. Most stories don’t actually build sympathy for characters and then suddenly change their intentions without warning. The meme of the spiteful creator is largely false: with a decently-written story, any dark turns are foreshadowed to a degree.
In SDFM, the allied Zentradi the most prominent and sympathetic, with the antagonist Zentradi being the ones opposed to the values of the series. There is nothing which suggests conventional storytelling is not in play: the characters that we see the most of, and who enjoy the things the audience is taught to value, are the ones who represent the views of the series. In this case, the allied Zentradi are meant to be “right”.
Furthermore, the alliance provided humanity with a means of defense and ensured they were not wiped out. If the series was going to show the audience that everything was pointless, the peace between the races would not produce this huge benefit that was impossible to achieve otherwise.
Viewers’ pessimism probably starts with episodes 28-36, the “aftermath” episodes, in which viewers spend some time hanging around the post-war Earth. During these episodes, allied Zentradi rebel against humanity, Warera, Rori, and Konda have difficulty finding work, Exsedol loses faith in his people’s position, and all of this gets no resolution.
However, these episodes were hastily written, added when the series was suddenly extended after having its planned run whittled down multiple times, and so might not represent a breakdown that was planned from the start.
Even if you take the aftermath episodes as in synch with the rest of the story, they still don’t solidly prove that the Zentradi/human alliance is self-destructive, since the alliance still endures. It's just showing that things aren't always perfect. And it’s actually good to tell a story that doesn't have everything end flawlessly, because it means the work is not simplistic.
Aaron Sketchley translated this portion of the Macross Chronicle, a guide to the Macross Universe released as a magazine.
"Combat" is "life" for the Zentraadi, who have had their fighting instinct strengthened, and although they lost their creator, they continued to fight in the direction of their instincts. However, their meeting with the human race became a turning point, and some of the Zentraadi who were members of the Bodol Main Fleet knew of culture and chose the road where they walk together with mankind. The strong thought control by the Protoculture is likely to have been cancelled by the emotional stimulus awakened by "songs".
The proverb "yesterday's enemy is today's friend" appears to have been communicated at the galactic level, as mankind and the Zentraadi, despite having crossed swords with each other at one time, chose coexistence. For the human race that advanced into the unknown galaxy, there is no partner as reassuring as the Zentraadi, who stood nearby. At any rate, that reassurance is assuredly because the mythical giants are comrades. (http://sketchleytranslation.host-ed.me/MCRworldguide/10AZentraadi.php)
Though the article says that Zentradi have had their “fighting instincts” strengthened, it is also eloquently describes the alliance as a good thing, further supporting the idea that a positive view of the Zentradi/human alliance is the official Macross byline.
When stories change what they first appear to be, they don’t suddenly crush what seemed like a completely earnest plot. Usually, the seeds of the story’s dissolution are planted early on. If Super Dimension Fortress Macross were that deeply cynical a series, it would have shown it long before the aftermath episodes.
Furthermore, good as it is, SDFM is an adventure-romance series designed partly to sell model kits. It's doubtful that it was intended to send audiences through a metal gauntlet, to present them with a sweet story and then violently overturn all their expectations. What we see at first is what we are meant to see. The allied Zentradi are meant to be sympathetic, their actions laudable and helpful, and there is nothing strong enough to invalidate this.
Internal conflict with allied Zentradi remains a common plot point in the Macross franchise, but it tends to be balanced out by positive examples in those same stories. It’s not a matter of a facade of positivity with the ugly truth being constant conflict: examples of positive Zentradi exist on the large and small scales both.
Yes, half-Zentradi Guld Goa Bowman of Macross Plus was an aggressive man who assaulted Myung and nearly killed Isamu, and one of his superiors attributes his actions to his heritage. However, the last thing could have been meant to be a discriminatory assumption and not to be taken literally by the audience.
Even if it was meant to be taken at face value, Guld is just one man, and the OVA/movie that also involves a celebration of the treaty, a thing to counteract Guld’s individual actions. Otherwise, this is still a world that has still benefitted from such contact. Guld could simply had bad genetic luck, and has the Zentradi equivalent of mental illness.
For the Temujin and his rebels, Macross Frontier also has the Folmo Mall and its happy Zentradi citizens, as well as Klan Klang (despite the unrelated issues with her character). Macross the Musiculture has Zentradi rebels, but things turn out to be more complicated than they first seem.
To have these conflicts constantly pop up without changing the status quo (in a good or bad way), is a little strange, but the writers are probably just repeating a motif as multimedia franchises always do. Macross in general has a problem with repeating motifs even when they might not make sense in context. That some allied Zentradi keep fighting humanity doesn’t seem to mean anything, including a degeneration.
Yet if the question of self-destruction comes up, the material that viewers get shows that the alliance was an ultimately positive thing. Yes, it hasn’t been completely perfect. But you know what? Good stories are told when freedom doesn’t come easily or without sacrifice. The story of the Zentradi is not perfectly written, but from what we do get, contact with humanity meant to be a net good, and not something that everyone would regret later.