Don't worry too much about the plot choices. Once you complete one of the two missions in each choice, you can play the other mission from the archive, and once you finish it, you can see the cutscene you missed. So the only thing to worry about is if the rewards for the mission differs.
(SPOILER)Ghosts and Spectres aren't that different, only one separate ability. Both of Ariel's missions offer the same reward, except for whether you get Zerg or Protoss research (and research points are overabundant anyway, you can easily max both trees). The air/ground is probably the biggest choice, and that's up to you, it only affects one more mission, the last one.
As for the ending:
(SPOILER)Watch the cutscene again. Kerrigan is not completely human. Her hair, at least, remains how it was when she was the Queen of Blades. I'm guessing that the Artifact fractured the control that was placed on her by the Overmind (which was in turn placed on the Overmind by the force behind the Hybrids). She has her human mind back, but remains Queen of the Zerg, and will have to gather them and forge the free Zerg into another army to strike at the hybrids.