The only TV commentary I read comes from the folks at ILX, and this rings particularly true: every explanation to date has been less an explanation and more a reveal of something else that requires explanation. The writers blog each episode, and it seems that the show-runners tend to throw in random scenarios which the room then has to fold into the narrative. This leads to very noticeable lurches where a character or plot-line is wrenched away from one location to the next, all in the service of thrills and spills. No doubt the velocity of the story is captivating, but when you step away from the vortex you're left with more questions than answers.
And as great as Maslany is, she can't make a character like Rachel breathe without the writers giving her a motivation to run with. An obsession with motherhood feels incongruous buried within a ruthless corporate clone: are all female leaders (the hated boss bitch) just sublimating their maternal instincts? The show as a whole is vague about the conflict it sets up between religious nuts and science freaks. Ostensibly, the heroes are fighting for a middle way between these extremes, defending their family against the assaults of ideologies that seeks to destroy it. But 'family' is also an ideology and subject to change in the face of social and technological change. This is ripe territory for the show to explore.
As an example: how will the mechanisation of childbirth transform motherhood? How will women feel towards their children when they are freed from constraints men have never had to bear (the process of pregnancy, birth, postpartum). The show steps back from such a future. Instead both Rachel and Helena (and the organisations that raised them) are obsessed with children and jealous of Sarah for having a daughter. Clones are facinating and valuable for still unarticulated reasons. Two seasons in, that's disappointing.