Quick comment ...

Yeah, I heard one wag state it as it was getting to the point with Kryptonian survivors that it seemed the only ones who did die were Jor-El and Lara.  The seemingly endless stream of survivors and artifacts from Krypton was already beyond ridiculous.

But I'd do it similar to the E-2 Krypton where only two survivors actually made it instead of inventing ways to gradually knock off the existing ones.  It's a reboot so take advantage of it.

Yeah, and keep Superboy in Superman's past.

I think that is a very narrow, seflish, and childish point of view, if you don't want to write stories with certain characters, just don't use them, there is no need to kill them off, just because you don't like them. Later on a new writer can come in and write great stories with characters that you didn't know what to do with. Why ruin it for everyone else?

Note that a very similar formula worked for the Superman movie, and the Golden Age Superman didn't find out about Krypton until he was an adult.  I don't think Superman has to know at birth that he's a Kryptonian orphan to feel like an outsider.  The powers and knowing he came from a mysterious rocketship will do that.

There's two ways I would approach this:

1: The first is to simply have things move forward after the Crisis. Supergirl will have died, but she would still have existed and be remembered for her sacrifice. The survivors of Kandor wouldn't have made Superman any less "special," especially since they were all located on Rokyn, which was in another dimension! I'd still use Krypto for the occassional strory, but I wouldn't use any of the other super-pets. I wouldn't kill them off or state that they never existed (that would be wrong), I just wouldn't use them. If some later writer wanted to he could write a story featuring them. I'd keep Brainiac in his cool cyber-organic form and feature him in many of Superman's stories, ditto for Mongul and Darkseid. I'd have Luthor "go straight" and form LexCorp (a Maggin invention)--I wouldn't have this go on as long as it did post-Crisis, though. It would last five years at the most and then scientist Lex would return.

As for the Phantom Zone criminals, I wouldn't have changed them much. They're a rich source of credible villains and gained great popularity after the Superman movies. Besides, it's just a cool idea. The Phantom Zone was such a creative idea and was far ahead of its time. It just makes sense that a society like Krypton would create such an effective way of dealing with hardened criminals, rather than just killing them.

As for the Earth-2 Superman and Earth-Prime Superboy, they'd still have adventures in their "paradise" world. There would be no fear of them crossing over to the mainstream DCU. Their adventures would be continued in their respective worlds, as if the Crisis never happened. This is my first approach, the second involves a reboot.

2: This approach is a full reboot. This would be different from DC's reboot in that there would not be pre-Crisis events that still happened in this continuity. Many would still remember them, however. Superman would, in fact, have dreams of the Pre-Crisis DCU, especially of Kara. This would be Alexander Luthor's gift to him. Barry Allen would still be the Flash and Wally West would be his sidekick, Kid Flash. Basically, things would start over from day one and heroes would actually age (slowly) in this reality.

As for the Earth-2 heroes, they would exist in the same paradise as the Earth-2 Superman. Their stories could still be told without any crossovers. The same is true for the Earth-Prime Superboy. The Legion would claim to be inspired by a "Superboy," but Kal will not have become Superboy in this continuity. But who would this Superboy be--the Legion doesn't know, as records from that time period are rare and often have contradictions. What is clear is that this Superboy DID exist, but where he came from is unknown. Eventually, I'd establish this Superboy as Kal's son (in a future that may or may not happen) and he would join the Legion (also a future that may or may not happen).

But what about Superman's origin? That's where there would be some big changes. Krypton would still be a utopia and all that, but the reason Superman has powers would be different. They would not come from Sol's energy or lighter gravity, but instead from Kryptonian evolution and genetic engineering (the fear that replaced radiation). Kryptonians would have evolved naturally to "leap tall buildings in a single bound" and have the other Golden Age Superman's powers. They would later improve these powers through genetic engineering. Krypton would still have a red dwarf star (called "Rao"), but their planet would be similar to our own in size and gravity. Once the Kryptonians started experimenting on themselves, the Guardians of the Universe "bonded" them to their planet, preventing them from leaving. They also gave the Daxamites their weakness to lead and the Martians their weakness to fire.

A word of the Daxamites, if I may. Daxam would be a sort of Counter-Krypton, hidden behind Rao. Their evolution would be similar to Krypton's, including their use of genetic engineering, only their powers would be inferior to Kryptonians. This is all unlikely, but not too unlikely if you consider the nature of Superman. As for Mon-El, Superman would never meet him in the present. Lar Gand would instead be a space explorer poisoned by lead and returning to Daxam. There he would be frozen until a cure could be found--it would be, one thousand years later by Brainiac 5.

Back to Krypton. The planet would adopt a very rational and altruistic state of mind. All decisions would be made by an elected council, of which Jor-El was a member. Jor-El discovered that Krypton's core was unstable after geological testing. Jor-El goes to the council with his findings, saying that he has discovered a way to remove the genetic bond between Kryptonians and their planet--unfortunately, it can only be accomplished by changing the genetic structure of unborn children (which Jor-El has done with his newborn son, Kal-El). Jor-El suggests having all pregnant women expecting to have their unborn children altered and then sent to other worlds. He suggests that the rest of Kryptonians place themselves in the Phantom Zone, which their children can rescue them from later. No one believes him, of course, and they even mock him. The story is the same from here, with Kal-El (and Kara Zor-El) being sent to Eartha (or Terra).

Kal-El is an infant when he's sent to Earth, and he spends almost two years in his spaceship. During this time, he is instructed by a program created by his father and mother. This teaches him morals and the history of his planet. Since he's still young, he only remembers his language, the names of his parents, his own name, and the name of his planet. Later, at age twelve, the ship downloads the full history of Krypton into his mind. Kal is found by the Kents and raised as Clark Kent. Shortly after he graduates high school, Jonathan Kent dies of a heart-attack. Kal soon builds the Fortress and alternates staying there and at college. He even equips the Fortress with Kryptonians artifacts stored in the Phantom Zone. When he turns twenty-five, he becomes Superman and joins the Daily Planet as Clark Kent.

As for villains, Lex Luthor is both a scientist and businessman. He practically made Metropolis "the city of tomorrow" with his inventions. He hates Superman because he is a threat to humanity's growth and is proof that Luthor isn't the greatest being on Earth. Brainiac is an android created by Vril Dox (and sees himself AS Dox) with a grudge against Earth for how they treated him when he crash-landed. He's now crazy and wants to control the universe "for its own good." Bizarro is a failed clone of Superman created by Lex. The creature is similar to Frankenstein's Monster. The Bizarro World will later re-appear, created by Mxyzptlk. Morgan Edge would still run Intergang, and the Toyman and Prankster would be members. Darkseid and Mongul would be the physical threats to Superman.

As for Clark Kent, he'd still be mild-mannered, shy, and unsure of himself. He wouldn't be a coward, however. Clark is non-confrontational. Lois would love Superman, while Lana would actually love Clark.

With Kandor, I have a very specific idea in mind. It would be populated not by Kryptonians or various aliens, but by the original sentient beings from Krypton--the Xan. The first Kandor was founded and inhabited by them, but during the war (no one knows how or who started it) with the Kryptonians, the city was banished into the Phantom Zone. This was caused by the Kryptonians and ended the war. Unfortunately, the Kryptonians never figured out a way to bring the city back or even view it. Superman encountered the city in a trip through the Zone, and even managed to be able to constantly view the city by linking it to a bottle similar to a bell-jar. He has sworn to restore the city, and has even given the Xan a reason to respect Kryptonians.

The only other surviving Kryptonian would be Kara Zor-El--Power Girl. Her ship would've taken a different route and she would've landed on Earth at about eighteen. She would adopt the Karen Starr identity and things would continue as normally. As for Krypto, he would still be here, but instead of a Kryptonian survivor, he'd be a super-powered canine created by Project Cadmus.

Whew. That's a lot to type. I actually have more ideas, but I'll leave it at that.