You don't have to scan stations piece by piece in Rebirth. Doing so gets you a temporary bonus but, if you don't already have some trade ships ready to take advantage of it, the bonus will run out before you can get anything out of it. (Though it is kinda fun if you put the thrusters on max and try to scan the whole thing without slowing.)
Drones are just little ships. I really don't use them much, personally. Hacking drones help to capture ships but that's really it. Hacking a station costs too much reputation for my style of play.
Trade reps essentially are trade satellites only they are on a per station basis. It does take WAY too long to get one, though, because of the small talk game you have to play to get one. Enter the
TAF mod. 80,000 credits (which isn't much by the time you start really needing lots of trade agents) and you've got your agent.
Hiring was also a massive pain as you had to go through the small talk just to find an NPCs stats - and the stats you got weren't even for the NPC you were speaking with! That's got a good mod, too:
Show Skills. Now everybody tells you their skills whenever you ask. You can still use the small talk to find the best at a given job if you want to save yourself sitting in a sector and phoning everyone up.
I really don't organize any fleets in Rebirth. I just send my trade ships all over known space doing deals and maybe assign some ships to stations to do trading. So I've got no clue how the fleet organization really works.
Gates don't give a good sense of scale. You go through one and end up somewhere else. When you go through a gate from sector A to B you have no idea if they are actually close in space or in a galaxy far, far away. With the highway system, you know how you got from A to B. (Though they were kinda long at first. Egosoft shortened them so they only take a few seconds now. Personally, I think they are a bit too short.)