When circumstances lead the protagonist of "Think Like a Dinosaur" to believe that teleportation is a form of murder, he faces a Moral Dilemma: defy the aliens and lose the opportunity his family so desperately needs, or obey them and have the death of an innocent human being on his conscience. The problem: the opportunity his family would get is to be teleported. So either i) teleportation is murder, in which case he should tell the aliens where to go stuff their "opportunity"; or ii) teleportation isn't murder, in which case, no harm, no foul. Either way, where is the moral dilemma?
In "Double Helix" Dr. Nodel has discovered a way to turn on Introns in human DNA. He starts experimenting on himself and then other humans. This eventually leads him to discovering an alien spacecraft. The episode spins this as a positive result of unrestrained scientific enquiry, but until the end, all he seemed to be doing was setting up his own cult with himself as leader.
Actually, the clip show episode "Better Luck Next Time" ended with the protagonists winning. Sure, they needed to do a Heroic Sacrifice, but they won.
In"Music of the Spheres", only young people could hear the perfect music in the strange noise, and all of the teenagers were being transformed. By the end of the episode, transformation somehow became a free choice for anyone. Did I miss something?
There is a mention of adapting the transformation signal to allow anyone to transform, in the montage of global preparations for the sun's shift.
If "Lithia" consists of only women, where are the children from?
It's probably related to how they kept the man cryogenically preserved for all that time. It's not really clear where the power to keep him preserved came from either, but if you accept that he stayed a popsicle all that time, you may as well accept that they also managed to preserve a ton of semen.