The first issue is size. How many passengers should be in that first generation? We're talking about the seed of a new population here, so it needs to be enough people to prevent genetic issues relating to inbreeding. A few dozen at the very least. Preferably over a hundred. The problem, though, is that the bigger the group, the harder it is to keep order. Which brings us to the next challenge...
Government and economy. What sort of system do they set up? A command economy? A free market? Something in between? How vital will production be? Will the passengers have to grow their own food, or will there be decades' worth of prepackaged meals on board? If the latter, then those rations will be used as money and as a means of oppression in much the same way that third-world dictators use food as a weapon. There's also the possibility of spoilage. Accidents happen, and all it would take is one incident to ruin part or all of the food supply. A freezer short-circuits, a plague of rats gets into the pantry, etc. Also, in this scenario, the population would have to be strictly controlled since the food supply is a zero-sum game. There are many ways such population control can go wrong. See China's One Child policy for a modern-day example.
If, instead of prepackaged food, they have to farm or herd, then some will produce more food than others due to differences in intelligence, education, work ethic, etc. This will result in some families being wealthier than others, and that will spark envy, and that will spark crime. The ship will need a police force. It will need laws and rules and courts. Human nature being what it is, bribes, blackmail, and threats will occur. Over the course of generations, the potential for riots and rebellions grows. There will be war. Perhaps even genocide.
Or perhaps a command economy is instituted, in which case all food is collected and everyone is promised an equal share from the communal pot. The problem with this is the same problem faced by the Plymouth Colony in 1623: famine and starvation. Here's Governor Bradford's account:
“The experience that was had in this commone course and condition, tried sundrie years, and that amongst godly and sober men, may well evince the vanitie of that conceite of Platos and other ancients, applauded by some of later times; -that the taking away of propertie, and bringing in communitie into a comone wealth, would make them happy and florishing; as if they were wiser then God. For this comunitie (so farr as it was) was found to breed much confusion and discontent, and retard much imployment that would have been to their benefite and comforte. For the yong-men that were most able and fitte for labour and servise did repine that they should spend their time and streingth to worke for other mens wives and children, with out any recompence. The strong, or man of parts, had no more in devission of victails and cloaths, then he that was weake and not able to doe a quarter the other could; this was thought injuestice. The aged and graver men to be ranked and equalised in labours, and victails, cloaths, etc., with the meaner and yonger sorte, thought it some indignite and disrespect unto them. And for mens wives to be commanded to doe servise for other men, as dresing their meate, washing their cloaths, etc., they deemd it a kind of slaverie, neither could many husbands well brooke it. Upon the poynte all being to have alike, and all to doe alike, they thought them selves in the like condition, and ove as good as another; and so, if it did not cut of those relations that God hath set amongest men, yet it did at least much diminish and take of the mutuall respects that should be preserved amongst them. And would have bene worse if they had been men of another condition. Let pone objecte this is mens corruption, and nothing to the course it selfe. I answer, seeing all men have this corruption in them, God in his wisdome saw another course fiter for them.”
Of course, the government could make those people work. But then you get into questions about what sort of world you're trying to build on the new planet and how slavery aboard the generation ship plays into that. If you're going to institute a feudal or caste system from the outset, then the only people you'll get to sign up for the trip will be those who want to be harsh taskmasters and those who are desperate enough to volunteer for serfdom. That's not a recipe for long-term success on an alien world. Might as well just stay on Earth.
One of my biggest beefs with a lot of SF is the portrayal of human in space colonies as little more than saintly robots. Where's the vice? Where's the envy and covetousness? Where's the corruption and oppression? Where's the violence? These things are endemic to the human condition. You can gather a few individuals together for a little while without much harm, as we currently do in situations like the International Space Station, but when you're talking about a generation ship, you've got too many people involved for too long a time to credibly omit humanity's worst characteristics. There's nowhere to go; everyone's stuck on the ship with each other. There's no social pressure relief valve. Given enough people and multiple generations in a confined space, there will be mass violence.
That's why I can't think of a way to make a generation ship work in a way that's socially satisfying. Humans are simply too flawed to make it work. On Earth, we can move to other countries, or move to the wilderness to live as hermits, and basically get away from each other if necessary. That can't happen on a ship.
If we go to the stars, I think it will have to involve cryo-sleep or ultra-fast travel or something else that allows us to get there in a single generation. The faster, the better.
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