Analysis by RevolutionStone
As a preface: I'm not really much of an anime or manga fan, but my friends were really into it in my college years so I decided to try out a few, and Trigun was one that actually held my interest for a bit because of the manga's more mature take on the idea of the Space Western and that it seemed to explore some very serious issues. Unfortunately, Writer Cop Out happened on almost all of said issues, and then I began to see the almost vindictive homophobic/transphobic streak. This review doesn't (mostly) apply to the anime except where they share the same issues, which actually does have fewer Unfortunate Implications simply due to its many Plot Holes (another issue entirely but...)
This analysis will be centered around the Unfortunate Implications and how they, like termites in a wooden house, undermined everything from the Aesop overload to even the story being enjoyable at all.
In general, the anime and especially manga seem to have an almost vindictive to the point of hate Bury Your Gays streak, possibly due to the writer's interpretation of his Roman Catholic faith at the time. As in, the way of resolving the obvious even if accidental Ho Yay between Wolfwood and Vash? Kill off one of them, in one of the most prolonged and brutally sadistic deaths of the manga or emphasizing his heterosexuality before he dies in the anime - the former being Bury Your Gays and the latter being Get Back in the Closet and Bury Your Gays. The canon gay Legato is a Depraved Homosexual who, as mentioned above, is a sadistic mass murderer driven to both his sexuality and murder via child abuse. The manga canon transgender Elendira is also a "Creepy Transsexual" / Depraved Bisexual stereotype, who suffers, again, one of the most sadistic deaths of the manga (far more so than anyone else). The Armored Closet Gay and creepily incestuous Knives somehow escapes any of this due to The Power of Love never mind he symbolically desires sex with his own brother (so being incestuously gay is A-OK as long as you sublimate it via violence), while an apparent way of purging The Hero Vash of the "taint" of Immortality Bisexuality is to make him Compensating for Something and either being creepily sexual toward or shy of women.
So you'd think that Meryl and Milly would prove that women can be just as badass as men? Nope! They are never shown being able to resolve any situation completely by themselves (despite allegedly being trained enough to survive as long as they have, most of their discussions center around the men or the things the men are doing. To give credit where credit is due, refreshingly, they at least aren't usually portrayed as intentional fanservice like most such female characters would be and Milly is one of the more positive portrayals of a plus-size woman in anime or manga even if she falls into the Big Fun and Big Eater tropes and is a bit of an airhead. Unfortunately, neither of them have very much page time or much writing outside of fandom to round them out more as characters, and in the end effectually they end up just as foils and backup for the men. All three female antagonists (I will consider Glendora female even if the manga is ambivalent on that, and Zadie is female in the manga) are also uniquely Broken Bird and some of the most mentally unstable out of a group of hired killers, Dominique having daddy issues and both her and Zadie being the personifications of Break the Cutie and Glendora being a sociopath. Almost all of the straight males among the mercenaries have other reasons than pure mental illness for their actions, and none of them have DaddyIssues or MommyIssues.
The female plants get it even worse - they are a Slave Race, which leads to the next point.
3: Happiness in Slavery? Yeah, got that too...