Here are my takes:
1) Nero goes about his business destroying planets and ships, and is about to destroy the Enterprise when he recognizes the ship (at least he seems to recognize the class before calling for a close-up; which makes sense since there were relatively few Constellation class starships back at this time period). Assuming that Spock was not on board would be more of a plot hole. He decides to take advantage of this, hurt Spock some more, and try to get the defense codes from Pike at the same time. Easy. Later when Nero says Kirk was a great man in another life, that doesn’t mean he did or didn’t know the extent of all the changes to the timeline that he has caused, just that he is terminating this one for Kirk.
2) Yeah, I didn’t like this either. I would have been happier with Spock Prime showing Scotty how to boost the warp speed on the shuttle (temporarily, before it burns out the warp coils or something) allowing them to almost catch up, then showing him how to beam aboard while at warp, but they didn’t do this. Instead, I think it is perfectly reasonable to posit that the Federation learns from the Dominion’s use of long distance transport (good catch, didn’t think about this one before) and makes use of it here. As for targeting the Enterprise, maybe they weren’t that far out. Does anyone remember if the Enterprise’s warp drive was damaged? When Kirk posits engineering crews could boost warp speed, Spock says (directly before kicking Kirk off the ship) that engineering crews are busy with repairs (radiation, etc.) and that Nero would have to drop out of warp for them to catch him. Could the Enterprise be moving at impulse for a time, or low warp, allowing Scotty and Kirk to catch up? For a mining ship, how fast can the Narada go anyway?
3) Standard movie hero survival skills: see also how long Scotty holds his breadth underwater, how Kirk survives the encounters on Delta Vega, how Kirk jump/falls 30+ feet basically onto his chest in the Narada, Sulu’s very useful parachute retractor (yet Kirk’s parachute cables break with the weight of two people), etc.
4) In TOS, they didn’t do site-to-site and they may have rarely done in-ship-to-transporter-pad. I think it is all about sensor accuracy and the transporter transceiver. Using internal sensors to lock-on to a person could be inadvisable at that time, or transporter transmitter/receiver wasn’t capable or reliable of locking onto people inside the ship.
5) While not done universally, as another poster said, Dax got the title in DS9 (“Behind the Lines”), and Data got the title in TNG (in Redemption part 2, Hobson says “We've arrived at the designated coordinates, Captain.” According to
http://tng.trekcore.com/episodes/scripts/201.txt).
As for other questions:
I think the Narada defeated or circumvented the defenses at Earth and was preparing to lower the drill and thus had their shields down when the Enterprise entered Saturn’s orbit.
Now how the Enterprise was able to move at warp speed into the atmosphere of Titan (?) without being torn apart (the deflector dish was named that for a reason), I don’t know. But the bird of prey also did it in Star Trek IV in reverse (seemed a mistake then too).