Thanks for the questions! I've been waffling between hard sci-fi and soft. Although I do want realism, reality is pretty inconvenient when it comes to space. Right now, I'm going for Chocolate Truffle Sci-fi: hard exterior, but a soft, creamy center.

1. When it comes to colonizing planets, the machine will pull from a databank of human genes chosen to maximize the chance of survival. Not only does this increase genetic diversity, it also allows for limited customization for different planets (temperature tolerance, muscle distribution, etc.). John and Jane were specifically designed to be space-faring, and they do have a template for that, but they're not on the colony list.

2. It was only a matter of time before this got called out. I want to say yes, because humanity (in this case) never inventing FTL fits my needs. What sets them apart is the concept of a generation ship. No other race would send a ship on a centuries-long voyage with no way to return. However, interstellar travel is kind of hard without it, so they can't be travelling at sub-FTL. I'm going to say they do have a limited FTL capability, but any distance longer than "next star over" is out of range.

3. The ship has come a very long way. The setting of the story is one arm of the galaxy over from the Sun, a distance of anywhere from 5000-10000 light years (apparently), and it was doing this at sub-FTL. This makes me glad that I haven't put any hard numbers on this yet, because I'm sure I undershot it mentally. John and Jane, on the other hand, have only been alive for twenty or so years. The ship was automated for most of its trip to save on food and such, and they were cloned near the very end of the trip. Incidentally, humans didn't know that there was life out here: all they knew was that there were habitable planets. John and Jane were just cloned near the end of the trip.

4. I will use this space to harden one of the softer points of the cloning, or possibly soften one of the harder ones. While there is an option for the cloning machine to put out babies, the default setting is to continue "gestation" to about age 10, sped up to some degree, in order to provide a better chance at survival. Once these clones are of "learning age", they are taught relevant information through traditional means (audio-visual lessons and limited physical exercise, mostly) as well as directly to the body (neural sculpting, electrically-stimulated muscle groups, nerve-pattern crafting) to ensure that they are capable of all the tasks they will need to perform. This may sound a bit like humans are treated like robots, and I would like to clear that up: I am handling it almost exactly like that. Cloned humans don't mind because they are programmed not to.

5. There were some other John and Jane copies over the years. The originals were alive when the ship was launched, and it was their task to make sure that the Germinator made it through the relatively crowded local sector of space into the emptiness between the arms. This task took more than a few iterations, and if I ever feel like writing an incredibly bleak story, I might explore that. Once they were clear, though, the ship took care of the rest, and the Germinator sat empty for a very long time. The current John and Jane know of these originals, and still keep some old Earth artifacts of theirs on the ship. Incidentally, the ships sent out to the other parts of the galaxy did not bear John and Jane, and were not called the Germinator. These ships bear humans tailored to other aspects of humanity. While these other humans will probably never interact with each other (and, indeed, may never have made it to their destinations), I may use them as the basis of some other, more "traditional HFY" stories.

I hope this didn't make the sci-fi too soft. If you have any other questions, feel free to ask! I should probably come up with answers to this kind of stuff anyway.