Normally I don't explain anything, too lazy I suppose, but there was some confusion mentioned, so I will try to cover some of what I think might be confusing. Sassiebone suggested the appearance of Harry Mudd, a funny villain who appeared twice on the old series. Where Khan is a sexy villain, Harry Mudd isn't. Chekov's remark about not keeping pets is a spoof at Ricardo/Khan's little pets on Alpha Ceti V in Wrath of….
Why I Like You McCoy
(Kirk in a fit of rage is trying to strangle Khan who has finally returned with the missing women. Khan is not defending himself, although Scotty and McCoy are trying to pull Kirk off Khan.)
McCoy: Jim, the cameras are on! Jim!
(Kirk stops and looks around at camera with deer in headlights look on his face)
Scotty: Not to mention you are scaring the irl-gays. (Carol and Uhura are clearly disturbed by Kirk's show of violence against Khan who isn't even trying to defend himself)
Kirk (letting smirking Khan go): I'm OK. I'm OK (sitting in his chair.)
(Mudd gives Khan back his chair but pulls up another so he can stay. Nero has eaten all the Oreos and is now chowing down on popcorn. Offers Khan some…accepted)
Scotty: Well, that was fun (helps self to popcorn…offers Khan some Romulan ale)
Kirk (getting his anger under control…not): I like Dr. McCoy because he's one of my best friends and is a hell of a lot smarter than he looks. I mean who would have thought of injecting Khan's blood into a dead tribble? I mean seriously! (Starts to get up and attack Khan again…Spock pulls him back into his chair)
Spock: Captain! Please!
Kirk (gritting his teeth): You think he only….did….Carol? Really?
(Spock looks at Uhura. She is not saying anything or even looking at him)
Spock: We will discuss this later. As for Dr. McCoy, I enjoy his corn fed bullshit and nonsensical hokum that half the time I don't understand.
Chekov: Uh…I like Dr. McCoy's nurses. Some real hot ladies.
Sulu: I like the fact Dr. McCoy respects my ability to assume command and demand respect from our enemies.
Uhura: I like Dr. McCoy's bedside manners.
Pike: I always found McCoy a little odd but harmless. Good doctor if he figured out how to bring Kirk back from the dead.
Adm. Marcus (Under his breath): If we sneak up on him we can all stab him to death before he knows it.
Pike: I'm pretty sure we won't be sneaking up on him. Why do you like McCoy?
Adm. Marcus: I don't like McCoy. Oh? Yes. I like the fact that McCoy…no….I don't like him.
Harry Mudd: I appreciate Dr. McCoy's brilliant taste in expensive things, including beautiful women which I just happen to have off camera on stage 3.
Khan (very casual almost too smooth): I like the way Dr. McCoy strapped me down and forced me to give blood to save his friend with no regards to the sanctity of my body.
Nero: I like his bag of magic bones. Oh, ex-wife sends her affections and wants to know when the next alimony check is coming in.
(How do you know my ex-wife? I knew that bitch was a demon from hell. This just proves it!)
Carol: I like his bravery and willingness to let me be saved when the torpedo clamped down on his arm.
Khan (to her): All you had to do was ask me how to release it. I would have told you.
Scotty: I like Dr. McCoy when he's been on a bender. The rest of the time he's a bloody nuisance.
Adm. Marcus: He's not looking. Let's do it now.