I can't argue many of those points, as a lot of those bothered me too.
The starship dropping off the cliff seemed like a silly excuse for a daring stunt (they needed to hit terminal velocity, but they would have hit the cliff at that speed, and it's not like jump starting a car ffs). The hologram was unlikely, but I was able to run with it.
The position of the nebula was a thought that crossed my mind too. Unexplored space right next door? I would have checked that in a basic survey before building a giant space station next to it. Couldn't have taken them more than a few hours to get back.
The Enterprise wasn't the only ship that could fly into the nebula, but they said they chose it because it had the best sensors of any of their ships, and Kirk seemed ready for adventure. Krall specifically wanted the Enterprise, so that was either luck, or the alien who came back nudged in that direction.
I have no problem believing Prime Spock carried that photo with him. It wasn't a big picture to carry around even in the Jellyfish ship, and being a physical photo in that era, it's also possible he had the photo with him on some kind of digital storage and had it printed out after he came back.
When Krall attacked, everyone was unprepared, and that was a huge swarm attacking. Were there any ships around capable of fighting them? Also I recall the swarm was affecting communications? They were caught unaware by a huge invasion force, and many of the people on the base seemed to be non Starfleet.
I assumed Krall stole the uniform after becoming more human so he could blend in with the crew and escape undetected.
Don't get me started on those little creatures. Not a good way to start off the movie, and it had to fight hard to get me back onside after that.
There are lots of good points there, many of which I thought myself, but come on, these are mostly ridiculously minor compared to the giant turds of logic the previous movies pulled. Do you want me to list them? Because I've got all night, and I'd need it.