I agree on the doctor/Isaac arc (some spoilers), I thought it was all absolutely ridiculous. Isaac is only there to gather data about humanity and characterised as unfeeling and non-emotional. Then the doc pulls a fit about how he doesn't have feelings for her and everyone on the ship is behind her, ostrasising Isaac. It felt like there was no logic at all to the situation and everyone had gone bananas. The Isaac breakup scene was hands down my favourite in the show.