Awesome thread here - tons of great ideas. = )
All right! Here's my take on it:
Krypton was a hostile environment to the Kryptonians - but they flourished eventually. Kryptonians were Golden Age -level of Physical and mental Marvel's, caused by centuries of genetic engineering*.
When exposed to red Sunlight Superman returns to Golden Age power-levels.
When coming to Earth, Superman's powers slowly increase to Post-Crisis levels.** Morrison-Morales Origin - it works well.
Clark Kent works at the Daily Planet, but it is nowadays a digital news-service, no print.***
Lex Luthor - An arms-dealer who has a global reach, his dirty hands in blackwater style security firms. Secretly fomenting conflict for personal gain and as a science experiment.
He is also a genius inventor and his unique advanced weapons are highly sought after on the black market.
Most of the continuity from New-52 would be carried over, similar to how Batman and Green Lantern always retains a good chunk of their history.
Superman's identity is secret. His adoptive Parents are dead.
The Phantom Zone returns to a Pre-Crisis style.
Return of the Love Triangle: Clark Kent is dating Lana Lang, who's suspected that he's Superman for some time. Meanwhile, he is drawn to Lois Lane in his Superman-guise, preventing his relationship with Lana from going anywhere. Eventually comes to a head and him and Lana breaks up. Foreswears relationships for a while after - focusing on work.
Kryptonite
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Green = physical death,
Red = Mental disease and disabilities, new variation every exposure. (i.e schizophrenia, depression, autism)
Blue= deadly to bizarro, temporary power-up for Superman
Black = unleashes dark nature, kryptonian most overcome with a mental battle
Gold = temporarily nullifies solar-powers
Magic is no longer more dangerous to Superman than to anyone else. I.e, he will have problems with a spell that causes neural pains when fighting crime, but he won't be hurt by a flame-ball created to harm a normal human.
*(If you recall, the genetic refining/engineering thing was actually a part of Byrne's reboot)
**(So a somewhat less powerful Superman than New-52)
***(for a look at what the new Planet would be like, check out the new Bugle that Bendis created:
)