Yeah. I remember the end of Red Son. Hate it!
Humans but that developed in another planet... hmm...
Look, in comics like in life practically anything is possible, but I think your theory is stretching it a lot. And here's why.
To say that kryptonians where humans but that developed a lot faster, would be not taking into account Krypton's own history. Kryptonians by their own historical accounts/records have had a highly advanced civilization for tens of thousands or even hundred of thousands of years. In each version and reboot they tell the story slightly different but in various versions it was said for example that the Eradicator was created by one of Superman's ancestor (Kem-L) 100.000 years in Krypton's past, and also they showed that kryptonian civilization even at the time was already a civilization more advance than our own. So in terms of time. It doesn't make much sense. True that no one knows exactly when our species came into being but what the story of Krypton tells us is that when primitive man was still banging rocks and clubs against one another, kryptonians where already an advance civilization.
You see in each version/reboot kryptonian civilization is either shown has being very old or that it has gone through many ages.
In the New 52 it was stated in beginning that kryptonians had never left their world because the immense gravity of the planet made it so, that if any organic being tried to leave the planet in a spaceship, the G forces were so great that hardly any astronaut survived to tell the tale. In fact they said that the clone wars was caused mainly because they started to create clones initialy to use has test subjects in their more advanced space programs but lately they started using them for medical experiments and who knows what else. Safe to say it ended in war and in the genocide of all clones. But! Sometime after that they showed Jor-El and Zod when they were much younger, and Jor had recovered and repaired an ancient spacecraft with FTL engines that dated back to some ancient age of Krypton, and he used that spacecraft to send various genetic samples of multiple lifeforms from Krypton to study the effects that the energy of different stars could/should have on kryptonian lifeforms. Jor-El even at the time theorized that something in their genetic makeup made their bodies able to generate and produce huge amounts of energy if only exposed to the right type of energies. That's how H'el was created. The most important point I absorved from that info was that kryptonians were highly advanced but, they already had been so or even greater in the past, in some age of kryptonians history that had been mostly forgotten.
Another problem with your theory is that although kryptonians look like us they're not like us in a lot of ways. Physiologically speaking their organs are different from ours, some placed in different locations and others are even more developed than ours. Also their genetic makeup is way more advanced than our own. Remember that creating a kryptonian clone is no easy task, and most of those who try, they fail completely or for the most part. Even Superboy (Kon-El) original version, was that he was a hybrid, made from half of Superman's and Lex Luthor dna, and even then Kon was not perfect. And the New 52 version is basicaly the same, difference being that Jon Kent was the biological son of Kal and Lois, and Kon is a hybrid created by both Kal and Lois dna mixed with a third strand of dna from Jon. It was Harvest attempt to create a cure for Jon that he had started to see has his own son.
Again this genetic incompatibility ruins your theory. Even if humans and kryptonians had for example been created from the same basic genetic matterial, even if it was in different planets, there shouldn't be so much incompatibility between humans and kryptonians. Yes there would always be some incompatibility, because thousands of years of evolution have their toll in any base genetic matterial. Here's an example. Imagine that we had already terraformed Mars, and you stayed on Earth while your clone was sent to Mars. Both of you would follow different paths. Mate with different women, and your decendants would do the same. That alone would cause enough genetic difference that in two generations if both you and your clones decendant met and had kids there would be minimal to almost no risk of inbreeding. In only two generations. But lets say it was a hundred or a thousand generations from now, and the same happened, there would still be no incompatibility, and if there was problems in conception, it would be mostly because of some genetic defect. Even hundred of thousands of years from now they would still be compatible. Another example would be if you went back in time lets say 50 thousand years and decided to mate with a woman from that time. She would still be able to get pregnant from you.
So lets add up the data. We know that a) Kryptonians have been around longer than we humans have b) Genetically we're incompatible. Adding this two, there's almost no room for your theory that humans and kryptonians have some basic common ancestor.
But! There is a way that humans and kryptonians might share more than looks. There had to have been some race that pre-dated both species and that race left their genetical matterial first on Krypton, and a lot of time afterwards did the same on Earth. That could explain some of the similarities while at the same explaining why physiologically and genetically both species have great differences.
But that's a long shot at best. Like throwing a sphere with a message to reach a determine person on another galaxy, at a specific time and place, billions of years in the future, and the sphere not hitting anything that might bounce it off course.
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