1) Krypton. The "born on Earth" thing seems a little too "have to run screaming away from the SA as much as possible" to me. It's okay to have an alien from another planet be born on said planet.
2) I actually like the idea of Krypton being destroyed by something other than natural causes. It makes more logical sense. I've come up with a number of scenarios that could do it.
3) I think the ship should at least deliberately aim for a continent so he doesn't end up underwater or something.
4) Yes, he absolutely should have powers from day one on Earth. Maybe this is just bias of my upbringing but pretty much all of the versions I grew up with, from the movie to all the cartoons, to the Superboy TV show, all have a Superman with powers from day one. I didn't even know there was an alternative until I was 16. Seriously. So this could just be childhood bias on my part, but yes, he should be some kind of "superbaby". Not necessarily flying around with his blanket wrapped around his neck like the old stories but maybe show him kicking in the side of his crib like in Superman 3 or something would be enough.
5) I wouldn't mind a Supergirl (or Powergirl if you prefer) but that's it. No cities, or pets, or half the population or whatever. Phantom Zone villains are fine as long as they get sent back there.
6) I prefer a recording in his ship that he asks to see. His parent reveal to him that he came to Earth from space and never hid this from him but the actual learning about his heritage has to be his decision. Maybe around puberty.
7) I've never been super (get it?) comfortable with a costumed Superboy. It just feels awkward because I don't see anyone choosing to call themselves that. That having been said, yes, he had adventures helping people in secret when he was younger like in Smallville.
8) Let me be very clear about this one: NOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOO!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!! The ONLY good version that has ever done this was the Smallville show. And even then it only worked because they made Smallville a suburb of Metropolis on that show. And having Clark save his life as the way they meet is the only way I see this working. Unless you plan to do it that exact way, there is no way to make this work and have it be even remotely believable.
9) I'll be honest, this one's not a deal breaker for me. I don't really care one way or the other. I prefer them alive but the assumption is they'll die at some point during his career anyway.
10) His mom. Period. This just works for me. He and Pa may have had a hand in coming up with ideas but ultimately she designs it.
11) It's his family crest but people just see an "S" so the name sticks. The only Earth bound explanation is that he's arrogant enough to call himself Superman. Which might have worked in the 1930s but seems a bit narcissistic today. And, no, it doesn't mean "hope".
12) I like the idea that he came up with the idea early on. Like his teen years. He worked for the school paper or something and really liked it. Something mundane like that. And also saw it as an opportunity to learn about events before they happen.
13) I prefer she finds out about a decade into his career. He chooses to reveal it to her because he trusts her. That having been said, she's not stupid. There's a very good chance she'd discover it on her own anyway. She knows how to do her job. Guy who looks like Superman with glasses on shows up with the first story on Superman? Yeah, that's gonna set off her BS detector.