As far as the Doctor’s Orders mission goes, I don’t have any real issue with the token gay and lesbian couples. This isn’t because “Yay, Inclusiveness!”, but because they’re bit characters. They spout their few lines of dialogue, then we never see or hear them again. If they were more important, I wouldn’t be as forgiving, but as it is, I’m willing to let it slide.
Also, I think it’s worth noting that the Samuels audio log actually illustrates two things: first, that even with Jack in charge, there are still some decent human beings working at Hyperion, and second, those decent human beings are treated just as badly as Jack’s enemies. If I’m remembering correctly, the only person we’ve seen working for Jack up to that point is Angel, and she’s passing herself off as an AI, so I don’t think that really counts. Samuels is the first we see of how Jack treats the people who work under him.
As for Athena, I don’t have issues with how her character was developed. To me, it seems pretty natural. Conscripted by Atlas as a child, she was trained as an assassin at the exclusion of all else. Sexuality either wasn’t important, or was outright forbidden. After her defection, she takes work as a mercenary. You don’t hire mercs to take them on dates; combine this with the fact that Athena was doing whatever it took to keep herself fed, and sex is going to be the last thing on her mind. In addition, neither she nor the people of Pandora are particularly social, so there’s little to bring the issue up outside of work.
Enter Janey. Janey isn’t Athena’s employer, so there’s no employer/employee disconnect. She has no issues hitting on Athena. Athena, however, has no idea how to respond to this, so she informs Janey that she’s going to focus on the job. At this point, Janey’s advances stop. It’s still pretty clear that she likes Athena, but she backs off and gives her room to both do her job, and let her get used to the fact that she likes her.
Now, during TVHM, Athena makes it clear that she was in a relationship with Janey (the game itself gives no clue how long the relationship lasted, though Tales from the Borderlands makes it clear that the relationship is ongoing). It’s worth noting, though, that the Athena that admits to being with Janey isn’t the one that the player is controlling; it’s the one relating the story. The player-controlled Athena is still focused on the job, and continues to be for the rest of the story. It’s only after leaving Jack’s employ that she decided to give a relationship with Janey a try. Even though she was focused on the job, she still had plenty of time to think about things.
To me, the thoughts going through Athena’s head aren’t focused around gender; they’re focused around the fact that someone actually finds her attractive. She doesn’t wear figure-revealing clothes, she doesn’t wear makeup, and she can kill you more ways than she can count. She’s not used to the idea that someone could find her attractive, and has no idea how to react to that, much less have an actual relationship with someone.
Even then, her relationship with Janey isn’t about making out or getting laid; it’s about learning more about herself. Even after her defection, she was still very much the assassin that Atlas made her; not surprising, since she needed to put food on the table, and that was pretty much her only marketable skill. Now, though, she has a chance to try other things out. Maybe Janey takes Athena to a movie, and she discovers that she really likes comedy. Maybe they go to a club, but have to leave inside an hour because Athena nearly ran a guy through for grabbing her ass.
Also, it’s not like Athena’s relationship with Janey is perfect. As I understand the events in Tales from the Borderlands, Athena is doing Bounty Hunting behind Janey’s back. Janey asked her to quit, so Athena is simply doing it behind her back instead of actually stopping. That’s not good for a relationship, no matter how long it’s been going. Athena is putting her relationship with Janey at risk, and may even be destroying it.
Anyway, I’ll wrap this up. It went on longer than I intended, and I think it’s rambling a bit.