While some of Wolfwood's weirder actions (before he really shows his true colors) can be handwaved as "it's a sci-fi setting, maybe the rituals have changed in the meantime", a hint to his real nature can be seen in his answer to Milly about his cross being "full of mercy" (as in, full of "quick mercy"—i.e. bullets): the Catholic "Hail Mary" prayer begins "Hail Mary, full of grace"...
Following the fight between Wolfwood and Chapel, Wolfwood turns his back on his defeated foe and casually saunters off, leading Chapel to kill Wolfwood by shooting him from behind. At first this troper thought it was a serious case of picking up the Idiot Ball, but then it's revealed in the next episode Chapel never wanted to kill Wolfwood. Legato used his People Puppet powers to force Chapel to do it. Chapel even tries to kill Legato in retribution, knowing it's a suicide mission, because Wolfwood spared his life and Chapel hates being indebted to someone. Having been raised by Chapel it was obvious Wolfwood would know the man's character, didn't seem so stupid anymore.
In the beginning of the story, it seems that Vash is just something of a Handsome Lech who has no idea how to behave around women. But once you get further in and realize he's really just Obfuscating Stupidity half the time, not to mention him pretending to be asleep just to avoid having sex, it becomes clear that, due to his loner status and shyness about his grotesquely scarred body, he's probably perfectly aware of what a deterrent that sort of behavior is to women and is doing it on purpose so they won't become too attached to or genuinely interested in him.
When the major antagonist, Legato Bluesummers, is introduced, he tells Vash that he has a bag that contains a lesson from him. A woman then runs into the square and says that her husband is dead. It's heavily implied that Legato has the man's head in the bag. It becomes even more disturbing when you realize he was eating a hot dog out of the same bag. He also fed another hot dog from that very same bag to a little girl. Just where did Legato get those hot dogs?
The anime is even freakier because the woman's husband isn't dead... but, as she keeps wailing, "he won't talk to her". Implying that Legato tore a living man's tongue out and stuffed it in a hotdog bun just so he would have something to snack on when he went to see Vash.
Near the end of the manga, it is mentioned that most of the towns have been destroyed by the ark and many did not survive. It's possible that many of the past characters of the day, such as Lina and Kaite, did not survive.
Actually, Lina and the old woman are shown to be alive and watching Milly and Meryl's TV broadcast in the last chapter.
One of the Epileptic Trees for how independent plants get born is engineers...fooling around with the plants. If this were the case, Steve would be the only feasible candidate for the twins' father. Ugh.
That theory doesn't make much sense. That'd make the twins half human. Also, plants have been shown not to be able to survive outside of their little globe things. They're like fish out of water. It's slightly possible, but really unlikely. Though I do wonder how they got born.
At the end of the anime, Vash "disables" Knives by shooting him in the joints, bandages his wounds, and starts the long trek to civilisation again, clearly hoping to finally "civilise" his brother. The thing is... Knives is not only a fanatical Omnicidal Maniac, he presumably has the same Psychic Powers that Vash's grafted arm gave to Legato. Powers which we see on screen as being powerful enough to make people kill each other in the most horrific ways. Just what is Knives going to do when he wakes up, crippled physically, in full possession of his psychic powers and surrounded by innocent human beings?
Well, if Vash's arm was what gave Legato the mind-control powers, maybe, odd as it seems given they're psychic powers, the ability comes from having use of one's arms? If that were the case, crippling Knives would render him at least considerably less harmful.
In the manga Vash is very unfazed by Wolfwood's death. Vash has lived for almost two centuries on a planet where death is a common occurrence. The reason why he's unfazed might be because he probably has seen many friends come and go throughout his life, and has learned to handle it better because he knows with his long life span on such a deadly planet, the death of those close to him will be a common occurrence, so to him, Wolfwood was just another dead friend.
Vash is actually very much affected by Wolfwood's death. He uses his Angel Arm, which shortens his lifespan every time he fires it, to blast a hole in the Ark as it floats by so Knives could see that Wolfwood had died.
Nightow occasionally forgets that having grown up on a desert-like planet, the characters wouldn't have the same comparisons and metaphors as us. A notable example is when Vash compares the sky to "the deep blue sea": you'd almost forget he grew up on a spaceship then on Gunsmoke and has never seen the sea...
He's read books, though. Even seen video, quite likely. (Knives had seen video clips of war and man's inhumanity to man in the manga.) Lots of people on Earth talk about the sea without any practical experience; it still has cultural currency on a desert world. He does do this, though. Especially as he declined to make the setting realistically inhabitable even with the plants, or balance the limited native biosphere into something comprehensible.
I.e. it consists of ostrich-horse tomas and giant sand worms. And little birds which must have hitched a ride like feathery rats or something, at least in the anime.
There are also littler native bugs. These seem to constitute an entire native ecology and share a hive mind.
There's something odd, about the character designs, I mean. In the manga covers, the characters are shown with tanned complexions (which you can chalk it to the fact that they're done on purpose, due the fact it's a desert planet, and thus, they should be tanned. Otherwise, it's to shown them having more vibrant colors). But in the anime, save for a few characters like Nicholas, Frank Marlon, B.D.N, and Legato. Everyone else is really pale, or have normal (i.e. healthy) white skin tone. Shouldn't they have darker skin?
