1) It wasn't a copy-paste given that the roles are reversed and it calls back to earlier developments in the film itself, and you're doing it a disservice to call it such. That said, if Khan wasn't involved then it would remind me more of NEM's take to emulate TWoK without "overtly" emulating TWoK...and that's not at all something I wish to see again.
2) That's my point though - changes would need to be made. The premise brought to me was "drop the name Khan but keep everything else". Any changes made to the film aside from that support my point that it's not that simple.
3) Personally I liked the phonecall, and Spock Prime made a point of saying that he wasn't generally comfortable discussing this sort of information. It seems likely that for a lesser (or perhaps less personal) threat he wouldn't have been so forthcoming. Anyway, if you know there's a future version of yourself out there that may have information about a current threat that you don't possess, it would be the height of irresponsibility -not- to ask them about it.
Since I didn't feel what transpired was a poor copy-paste job but rather a fairly respectful homage that maybe on occasion was a bit too on-the-nose, the idea of dancing around Khan without making it obvious that that's exactly what they're doing strikes me as...dubious. Which is what I've been saying the whole time. Maybe they could have made it happen, but since we don't have such a version of the film to look at for comparison, I'll say I'm glad they didn't try to pull off that kind of dance. It's been my experience that Trek writing frequently doesn't handle that particular kind of delicacy very well.
Anyway, we have exactly two movies now to use as a baseline for how the series might progress, so to conclude it's never going to do anything original with that degree of evidence seems shortsighted.
If memory serves, the first two episodes of TNG weren't exactly breathtaking either..but they did lay the groundwork for, pardon my French, some pretty cool shit to come.