The really fail-y thing about that episode, to me, was making Mary evil in the first place. It would have been pretty interesting to have Tosh fall in love with an alien in a female form. Maybe if Mary had initially wanted to get her transporter back, but found that she loved Tosh and wanted to stay with her... that would have been such an awesome ongoing relationship storyline. Plus, I thought Tosh deserved to have someone care about her romantically who wasn't a frozen soldier or a memory alien.

We don't really know the "gender" of Mary's alien form, but she presented as a human woman in her relationship with other people, so for all purposes, Tosh found herself with a woman, which raised orientation issues on her end. It could have also raised the concept of discrimination - I could see Owen or others not trusting Mary, knowing that she wasn't really human. (We know Gwen would probably give her the benefit of the doubt and Jack's had sex and probably relationships with aliens, so why are all of the aliens on TW such evil assholes, or even if they're not intentionally evil, they're harmful to humanity?)

Missed opportunity for an interesting story, IMO.