Great comments by everyone!! Spoilers below for Season 9:
My feeling so far is the scientist/soldier Sam is finally coming into her own in Prototype and The Fourth Horseman and I am very happy about that. I was concerned that we wouldn't see much of her in these two episodes, but it was the opposite. Sam is her competent brilliant self, coming up with solutions and working with the team. Ironically, Sam seems more of a leader and has more "command" presence so far this season than in season 8 when she was supposed to be the leader! I think TPTB copped out here, but maybe Scifi said, we need a new male lead and he has to be the leader. Ridiculous. So the writers are trying to walk a fine line here about what makes actual sense storywise and pleasing suits. Regardless of all of this, Sam is coming across as very competent and great at command that she is given.
I did not have a problem with Landry and Mitchell and how they react to her. It is a bit refreshing to have the Landry/Carter relationship be a bit unknown. It is clear to me that Landry and Mitchell respect her---almost all of Mitchell's interactions with her have been very respectful--he trusts her and defers to her expertize as he should. I think Landry's behavior toward her in the conference room is the way BBridges is playing Landry---he's more gruff and we really don't know him yet. He is not Hammond and I don't want him to be. I think Landry respects Sam but Hammond and Sam have a very different type relationship. Sam has to figure Landry out a bit, and I don't mind that. In most of their interactions, Landry clearly respects her and I think he did even if the scene in the conference room. It seems that the writers are trying to squeeze in "Jackisms' anywhere they can. They gave these jackisms to Landry and Mitchell in this scene and they really didn't need to because it doesn't work as well. (Often the writers have been giving Daniel Jackisms too---sometimes it works, sometimes it doesn't). But overall, when I look at all of Landry/Sam and Mitchell/Sam interactions, I see respect.
Maybe I'm in the minority here, but I really liked the Orlin/Sam interaction, and I think that part II is going to be interesting because Sam does care for Orlin and she sees what is happening to him. I think that AT and Bright played their scenes very well, and I don't think bringing up this personal side of Sam is at all hurting her character. I think this because Orlin has a legitimate place in the storyline. He is an Ancient, he did come to visit Sam before, he did love her, and now Earth is in trouble and he can help. This is more than personal for Sam---this is going to be her struggle for caring about Orlin and his health, and the issue of caring for the greater good and finding a cure. This struggle will be even more compelling because Orlin is in a child form. Orlin fits the story arc here, and Sam is a part of it. We've learned alot so far from Orlin about the Ori and this is important to the storyline. I loved the way AT protrayed being uncomfortable with Orlin professing his love again, yet she also really does care for him. And I don't think Sam is going to actually say anything to Orlin about her personal life---it would be inappropriate in that context and unnecessary. Also, I do think that Orlin and Sam did have an "intimate relationship" but not of the sexual kind--something beyond that--so intimate in a more spiritual sense. I don't think that "fact" negates Sam and Jack's interest in each other at all. Orlin/Sam and Jack/Sam are like apples and oranges---not even comparable. Now orlin is back and there is a good reason why he is back.
I also loved Sam and Dr. Lee. Dr. Lee sees Sam in a different way than anyone else and I think he is jealous of her (but not in a bad way). They are great together and I hope to see more of their interaction. It gives Sam a chance to be a little funny and you can see the science rivalry going on.
My feeling so far is the scientist/soldier Sam is finally coming into her own in Prototype and The Fourth Horseman and I am very happy about that. I was concerned that we wouldn't see much of her in these two episodes, but it was the opposite. Sam is her competent brilliant self, coming up with solutions and working with the team. Ironically, Sam seems more of a leader and has more "command" presence so far this season than in season 8 when she was supposed to be the leader! I think TPTB copped out here, but maybe Scifi said, we need a new male lead and he has to be the leader. Ridiculous. So the writers are trying to walk a fine line here about what makes actual sense storywise and pleasing suits. Regardless of all of this, Sam is coming across as very competent and great at command that she is given.
I did not have a problem with Landry and Mitchell and how they react to her. It is a bit refreshing to have the Landry/Carter relationship be a bit unknown. It is clear to me that Landry and Mitchell respect her---almost all of Mitchell's interactions with her have been very respectful--he trusts her and defers to her expertize as he should. I think Landry's behavior toward her in the conference room is the way BBridges is playing Landry---he's more gruff and we really don't know him yet. He is not Hammond and I don't want him to be. I think Landry respects Sam but Hammond and Sam have a very different type relationship. Sam has to figure Landry out a bit, and I don't mind that. In most of their interactions, Landry clearly respects her and I think he did even if the scene in the conference room. It seems that the writers are trying to squeeze in "Jackisms' anywhere they can. They gave these jackisms to Landry and Mitchell in this scene and they really didn't need to because it doesn't work as well. (Often the writers have been giving Daniel Jackisms too---sometimes it works, sometimes it doesn't). But overall, when I look at all of Landry/Sam and Mitchell/Sam interactions, I see respect.
Maybe I'm in the minority here, but I really liked the Orlin/Sam interaction, and I think that part II is going to be interesting because Sam does care for Orlin and she sees what is happening to him. I think that AT and Bright played their scenes very well, and I don't think bringing up this personal side of Sam is at all hurting her character. I think this because Orlin has a legitimate place in the storyline. He is an Ancient, he did come to visit Sam before, he did love her, and now Earth is in trouble and he can help. This is more than personal for Sam---this is going to be her struggle for caring about Orlin and his health, and the issue of caring for the greater good and finding a cure. This struggle will be even more compelling because Orlin is in a child form. Orlin fits the story arc here, and Sam is a part of it. We've learned alot so far from Orlin about the Ori and this is important to the storyline. I loved the way AT protrayed being uncomfortable with Orlin professing his love again, yet she also really does care for him. And I don't think Sam is going to actually say anything to Orlin about her personal life---it would be inappropriate in that context and unnecessary. Also, I do think that Orlin and Sam did have an "intimate relationship" but not of the sexual kind--something beyond that--so intimate in a more spiritual sense. I don't think that "fact" negates Sam and Jack's interest in each other at all. Orlin/Sam and Jack/Sam are like apples and oranges---not even comparable. Now orlin is back and there is a good reason why he is back.
I also loved Sam and Dr. Lee. Dr. Lee sees Sam in a different way than anyone else and I think he is jealous of her (but not in a bad way). They are great together and I hope to see more of their interaction. It gives Sam a chance to be a little funny and you can see the science rivalry going on.
If there is such a position out there, I'm DEFINITELY in the wrong line of work. 
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