Janeway's decision to destroy the Array becomes more understandable when one remembers that there's no guarantee they'd have figured out a safe way to use this extremely dangerous alien technology, that killed half of each crew just on the first trip when it was (presumably) working properly.
Captain Janeway mentions having served with Tom's father. Given that she's shown to be "on a first name basis" with several Starfleet admirals, it's not too much of a stretch that she's doing an under-the-table favor for Admiral Owen Paris by giving his son a chance to redeem himself.
The holo-farm on the Array. A line later on from Tuvok clarifies that the Maquis were also treated to a holographic "waiting room." Many if not most of the Maquis were farmers. The Caretaker probably designed that farm initially for them.
The Caretaker only left a five-year supply of food for the Ocampa. Even though they age about ten times as fast as humans, that still means they only have the equivalent of a 50 year supply, barely enough for a single generation! Better hope that newfangled horticulture holds up!
Sam Wildman presumably had her abdomen impaled by the Caretaker's needle while she was pregnant with Naomi. Even though "Naomi" would have been microscopic at this point, Q only knows what the Caretaker was doing to the womb that the fetus would be developing in for the next year-and-a-half.
Following on from some Fridge Brilliance above... if Tom's father really did get Captain Janeway to offer Tom a deal to get him out of jail, then it follows that Admiral Paris spent the next six years thinking he got his own son killed.
